Question

exomeCopy error in col name

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chiara.rigobello • 0

@chiararigobello-15139

Last seen 6.7 years ago

Hi , I'm having an error in exomeCopy when I computate fit.

(No previous error, following the vignette, and with provided data).

> fit <- exomeCopy(counts[seqnames(counts) ==
+ "chr1"], sample.name = "BIR", X.names = c("log.bg",
+ "GC", "GC.sq", "width"), S = 0:6, d = 2)
Error in exomeCopy(counts[seqnames(counts) == "chr1"], sample.name = "BIR", :
sample.name is not a column in rdata.

I've tried to check all objects containing name, but probably I've missed something!

any suggestion is appreciated

chiara

exomecopy • 872 views

ADD COMMENT • link updated 6.7 years ago by Michael Love 42k • written 6.7 years ago by chiara.rigobello • 0

score 0 · Answer 1 · 2018-03-02

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Michael Love 42k

@mikelove

Last seen 3 hours ago

United States

Can you show that BIR is in fact a name in the mcols of the object? (That message is somewhat outdated because we no longer use RangedData but now GRanges.)

ADD COMMENT • link 6.7 years ago Michael Love 42k

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I know that the problem is in that.

If I look at

colnames(mcols(counts))
[1] "BIP" "BIR" "BIQ" "AWI" "AWJ" "AWK" "AWL" "AWM"
[9] "BQ0" "GC" "GC.sq" "bg" "log.bg" "wdth" "bg.var"

(That message is somewhat outdated because we no longer use RangedData but now GRanges.) --> how can I verified this?

Sorry, but I'm a self-taught in bioinformatics.

thanks for your help

ADD REPLY • link 6.7 years ago chiara.rigobello • 0

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And are you using version 1.24 (the most recent version)?

ADD REPLY • link 6.7 years ago Michael Love 42k