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nac
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@nac-4545
Last seen 10.3 years ago
Hi,
I sent this email a while back and didn't get any reply, could anybody
help please?
thanks
Nathalie
-------- Original Message --------
Subject: seeking help on cghMCR pleeeease
Date: Mon, 12 Dec 2011 14:17:58 +0000
From: Nathalie Conte <nac@hinxton.sanger.ac.uk>
To: bioconductor at r-project.org
HI,
I am using cghMCR and I would need some advice on the software
behaviour. I don't seem to get any different results when I change the
gapAllowed parameter.
I have used DNAcopy to create a segmented data for all my samples.
Then
I choose to use cghMCR to get common alterations between my samples.
These are all arguments from the package doc(latest version):
segments is a data frame extracted from the "output"
element
of the object
returned by segment of the package DNAcopy or getSegments
gapAllowed is an integer specifying low threshold of base
pair number to
separate two adjacent segments, belower which the two
segments will be joined
as an altered span
alteredLow is a positive number between 0 and 1 specifying
the lower resh-
old percential value. Only segments with values falling
below this threshold are
considered as altered span
alteredHigh is a positive number between 0 and 1
specifying
the upper resh-
old percential value. Only segments with values falling
over
this threshold are
considered as altered span
recurrence is an integer between 1 and 100 that specifies
the rate of occur-
rence for a gain or loss that are observed across sample.
Only gains/losses with
ocurrence rate grater than the threshold values are
declared as MCRs
spanLimit is an integer that defines the leangh of
altered
spans that can be
considered as locus. It is not of any use at this time
thresholdType is a character string that can be either
"quantile" or "value"
indicating wether alteredLow or alteredHigh is quantial
or
actual value
In my analysis, I have used cghMCR with threshold value log2R of low
-0.25 and high =0.25 , a spanLimit of 2.10^7 and I have tried several
gapAllowed values, 5, 500 , 5000 and 50000 .Each time I used the MCR
function to identify the minimum regions. I have put an example of
each
results only on 25 lines of chromosome 4 to avoid massive sized files
(see attached) , but basically whatever the gapAllowed size i get the
same MCRs at the end for all postitions. I would expect this to vary
as
segments should be fused together differently given this parameter..
Could you please help with this and advise on what I might be doing
wrong?
Is spanLimit any use? in the doc, It is written "It is not of any use
at this time"??
Another point, the gapAllowed is specified " is an integer specifying
low threshold of base pair number " is the unit in base pair number,
in
several examples it seems that the units are in kb???
thanks a lot ,
code for gapAllowed=5
##get the cghMCR function with these parameters
cghmcr0.25T_5k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5,
gapAllowed = 5, alteredLow = -0.25,alteredHigh = 0.25,
spanLimit=20000000,recurrence=2,thresholdType=c("value"))
##identify the MCRs
mcrs0.25T_5k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5k_2_20M_sdundo1.5)
mcrs0.25T_5k_2_20M_sdundo.bind1.5 <-cbind (
mcrs0.25T_5k_2_20M_sdundo1.5[, c ( "chromosome", "status",
"loc.start",
"loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] )
write.table(mcrs0.25T_5k_2_20M_sdundo.bind1.5,
file="PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5.txt", sep="\t",
row.names=F)
PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5k_
2_20M_sdundo.bind1.5.txt",
sep="\t", header=T)
##only 25 lines of chromsome 4
test.5k=head(PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5k_2_20
M_sdundo.bind1.5==4,],25)
##attached data
write.table(test.5k, file="test.5k.txt", sep="\t")
code for gapAllowed=500
cghmcr0.25T_500k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5,
gapAllowed = 500, alteredLow = -0.25,alteredHigh = 0.25,
spanLimit=20000000,recurrence=2,thresholdType=c("value"))
mcrs0.25T_500k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500k_2_20M_sdundo1.5)
mcrs0.25T_500k_2_20M_sdundo.bind1.5 <-cbind (
mcrs0.25T_500k_2_20M_sdundo1.5[, c ( "chromosome", "status",
"loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171]
)
write.table(mcrs0.25T_500k_2_20M_sdundo.bind1.5,
file="PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5.txt", sep="\t",
row.names=F)
PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5
00k_2_20M_sdundo.bind1.5.txt",
sep="\t", header=T)
test.500k=head(PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_500
k_2_20M_sdundo.bind1.5==4,],25)
write.table(test.500k, file="test.500k.txt", sep="\t")
code for gapAllowed=5000
cghmcr0.25T_5000k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5,
gapAllowed = 5000, alteredLow = -0.25,alteredHigh = 0.25,
spanLimit=20000000,recurrence=2,thresholdType=c("value"))
mcrs0.25T_5000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5000k_2_20M_sdundo1.5
)
mcrs0.25T_5000k_2_20M_sdundo.bind1.5 <-cbind (
mcrs0.25T_5000k_2_20M_sdundo1.5[, c ( "chromosome", "status",
"loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171]
)
write.table(mcrs0.25T_5000k_2_20M_sdundo.bind1.5,
file="PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5.txt", sep="\t",
row.names=F)
PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_
5000k_2_20M_sdundo.bind1.5.txt",
sep="\t", header=T)
test.5000k=head(PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5
000k_2_20M_sdundo.bind1.5==4,],25)
write.table(test.5000k, file="test.5000k.txt", sep="\t")
code for gapAllowed=500000
cghmcr0.25T_500000k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5,
gapAllowed = 500000, alteredLow = -0.25,alteredHigh = 0.25,
spanLimit=20000000,recurrence=2,thresholdType=c("value"))
mcrs0.25T_500000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500000k_2_20M_sdund
o1.5)
mcrs0.25T_500000k_2_20M_sdundo.bind1.5 <-cbind (
mcrs0.25T_500000k_2_20M_sdundo1.5[, c ( "chromosome", "status",
"loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171]
)
write.table(mcrs0.25T_500000k_2_20M_sdundo.bind1.5,
file="PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5.txt", sep="\t",
row.names=F)
PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25
T_500000k_2_20M_sdundo.bind1.5.txt",
sep="\t", header=T)
test.500000k=head(PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5[PT_mcrs0.2
5T_500000k_2_20M_sdundo.bind1.5==4,],25)
write.table(test.500000k, file="test.500000k.txt", sep="\t")
sessioninfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] cghMCR_1.10.0 limma_3.4.5 CNTools_1.6.0
genefilter_1.30.0
[5] DNAcopy_1.22.1
loaded via a namespace (and not attached):
[1] annotate_1.26.1 AnnotationDbi_1.10.1 Biobase_2.8.0
[4] DBI_0.2-5 RSQLite_0.9-1 splines_2.13.0
[7] survival_2.35-8 xtable_1.6-0
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
-------------- next part --------------
"chromosome" "status" "loc.start" "loc.end"
"mcr.start" "mcr.end" "samples" "X"
"1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6
b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146
9518784.txt" 7
"1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h
_PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P
PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_
17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt"
7
"1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_
15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_
17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_
251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_
251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_
24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_
24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
"1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_
11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
-------------- next part --------------
"chromosome" "status" "loc.start" "loc.end"
"mcr.start" "mcr.end" "samples" "X"
"1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6
b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146
9518784.txt" 7
"1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h
_PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P
PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_
17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt"
7
"1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_
15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_
17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_
251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_
251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_
24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_
24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
"1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_
11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
-------------- next part --------------
"chromosome" "status" "loc.start" "loc.end"
"mcr.start" "mcr.end" "samples" "X"
"1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6
b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146
9518784.txt" 7
"1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h
_PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P
PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_
17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt"
7
"1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_
15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_
17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_
251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_
251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_
24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_
24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
"1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_
11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
-------------- next part --------------
"chromosome" "status" "loc.start" "loc.end"
"mcr.start" "mcr.end" "samples" "X"
"1236" 4 "gain" 3012291 155625629 3012291 3104649 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6
b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146
9518784.txt" 7
"1237" 4 "gain" 3012291 155625629 3104649 3271379 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt,
PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h
_PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1238" 4 "gain" 3012291 155625629 3271379 3335299 "PKBL_
11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P
PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1239" 4 "gain" 3012291 155625629 3335299 3353037 "PPAB_
17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1240" 4 "gain" 3012291 155625629 3353037 3804119 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1241" 4 "gain" 3012291 155625629 3804119 3810172 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1242" 4 "gain" 3012291 155625629 3810172 3825707 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1243" 4 "gain" 3012291 155625629 3825707 3882946 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt"
7
"1244" 4 "gain" 3012291 155625629 3882946 5377872 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1245" 4 "gain" 3012291 155625629 5377872 5386981 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1246" 4 "gain" 3012291 155625629 5386981 5656761 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1247" 4 "gain" 3012291 155625629 5656761 5661982 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1248" 4 "gain" 3012291 155625629 5661982 6045858 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1249" 4 "gain" 3012291 155625629 6045858 6055446 "PPAB_
15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1250" 4 "gain" 3012291 155625629 6055446 6210181 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1251" 4 "gain" 3012291 155625629 6210181 6273347 "PPAB_
17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT
_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518
575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt"
7
"1252" 4 "gain" 3012291 155625629 6273347 6649553 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1253" 4 "gain" 3012291 155625629 6649553 6655783 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_
251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1254" 4 "gain" 3012291 155625629 6655783 6817158 "PPAB_
17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_
251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187
84.txt" 5
"1255" 4 "gain" 3012291 155625629 6817158 6941107 "PPAB_
24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1256" 4 "gain" 3012291 155625629 6941107 7274363 "PPAB_
24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2
51469518784.txt" 3
"1257" 4 "gain" 3012291 155625629 7274363 7795963 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2
51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4
"1258" 4 "gain" 3012291 155625629 7795963 8405887 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
"1259" 4 "gain" 3012291 155625629 8405887 8478629 "PKBL_
11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_
251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186
04.txt,PPAC_4_1c_PT_251469518784.txt" 6
"1260" 4 "gain" 3012291 155625629 8478629 9241084 "PPAB_
24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2
51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878
4.txt" 5
