Question

gcpapc package fails at bindWidth step

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dfinkels64 ▴ 10

@dfinkels64-14339

Last seen 7.1 years ago

Hi,

I'm trying to test gcapc on my own bam file. It works fine on the system file.

The command and error are below, any suggestions are welcome:

> bindWidth(coverage, range = c(50L, 500L), step = 50L, odd = TRUE)
Starting to estimate bdwidth.
Error in bindWidth(coverage, range = c(50L, 500L), step = 50L, odd = TRUE) :
bdwidth: coverage is not a list of 2 elements

bioconductor gcapc • 1.3k views

ADD COMMENT • link 7.1 years ago dfinkels64 ▴ 10

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Sorry the last was wrong HERE is the error I'm having:

bindWidth(cov, range = c(50L, 500L), step = 50L, odd = TRUE)
Starting to estimate bdwidth.
...... Cycle 1 for bind width estimation
Error in seq.default(range[1], range[2], step) :
'from' must be a finite number

ADD REPLY • link 7.1 years ago dfinkels64 ▴ 10

score 0 · Answer 1 · 2017-11-07

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dfinkels64 ▴ 10

@dfinkels64-14339

Last seen 7.1 years ago

Solved it: header needed to change: no NT sequences

ADD COMMENT • link 7.1 years ago dfinkels64 ▴ 10

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Hi! I met the same error when I tried gcpapc. Could you please share your experience? Thank you!

ADD REPLY • link 5.3 years ago hzgdtd • 0

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My bam file DOES NOT have any NT sequences, and YET I have the same error message while using gcapc 1.6.0:

cov <- read5endCoverage(BamFile)

The cov object:

cov $fwd RleList of length 194 $chr1 integer-Rle of length 248956422 with 1284213 runs Lengths: 17461 1 31808 1 12713 1 ... 1 406 1 283 1 26246 Values : 0 1 0 1 0 1 ... 1 0 1 0 1 0

$chr2 integer-Rle of length 242193529 with 1183193 runs Lengths: 11293 1 270 1 90 1 106 ... 24631 1 1268 1 13656 1 22086 Values : 0 1 0 1 0 1 0 ... 0 1 0 1 0 1 0

$chr3 integer-Rle of length 198295559 with 1679261 runs Lengths: 11802 1 330 1 14 1 ... 1 4691 1 16566 1 105105 Values : 0 1 0 1 0 1 ... 1 0 1 0 1 0

$chr4 integer-Rle of length 190214555 with 901013 runs Lengths: 19783 1 25 1 12 1 3180 ... 280 1 1709 1 9 1 32902 Values : 0 1 0 1 0 1 0 ... 0 1 0 1 0 1 0

$chr5 integer-Rle of length 181538259 with 1102613 runs Lengths: 11989 1 1152 1 30 1 34 ... 7914 1 1154 1 96376 1 78386 Values : 0 1 0 1 0 1 0 ... 0 1 0 1 0 1 0

... <189 more elements>

$rev RleList of length 194 $chr1 integer-Rle of length 248956422 with 1281885 runs Lengths: 17549 1 47136 1 35014 1 ... 1 233 1 31 1 28032 Values : 0 1 0 1 0 1 ... 1 0 1 0 1 0

$chr2 integer-Rle of length 242193529 with 1184149 runs Lengths: 11712 1 97 1 398 1 1812 ... 10899 1 16421 1 225 1 35424 Values : 0 1 0 1 0 1 0 ... 0 1 0 1 0 1 0

$chr3 integer-Rle of length 198295559 with 1678265 runs Lengths: 12060 1 30 1 558 1 ... 1 21137 1 26 1 105128 Values : 0 1 0 1 0 1 ... 1 0 1 0 1 0

$chr4 integer-Rle of length 190214555 with 900249 runs Lengths: 10742 2 6145 1 1241 1 1772 ... 4 2 17 1 18041 1 14761 Values : 0 1 0 1 0 1 0 ... 0 1 0 1 0 1 0

$chr5 integer-Rle of length 181538259 with 1103893 runs Lengths: 12088 1 61 1 239 1 ... 1 3436 1 8709 1 225820 Values : 0 1 0 1 0 1 ... 1 0 1 0 1 0

... <189 more elements>

And then:

bdw <- bindWidth(coverage = cov, range=c(50L,300L), step=10L) Starting to estimate bdwidth. ...... Cycle 1 for bind width estimation Error in seq.default(range[1], range[2], step) : 'from' must be a finite number

Any solution to that?

ADD REPLY • link 5.1 years ago rmendez • 0