Question: gcpapc package fails at bindWidth step
0
gravatar for dfinkels64
2.1 years ago by
dfinkels640
dfinkels640 wrote:

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 • 421 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by dfinkels640

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 REPLYlink written 2.1 years ago by dfinkels640
Answer: gcpapc package fails at bindWidth step
0
gravatar for dfinkels64
2.1 years ago by
dfinkels640
dfinkels640 wrote:

Solved it: header needed to change: no NT sequences

ADD COMMENTlink written 2.1 years ago by dfinkels640

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

ADD REPLYlink written 3 months ago by hzgdtd0

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 REPLYlink written 22 days ago by rmendez0
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