Question: Problem in using covplot ChIPseeker
0
gravatar for vasudha.sharma
6 months ago by
vasudha.sharma0 wrote:

Hi,

I am trying to use covplot from ChIPseeker package to plot the coverage of MACS Narrowpeak output file and I am getting following error:

covplot(peakIMR90MACS, weightCol="V5") Error in .normargshiftor_weight(weight, "weight", x) : 'weight' must be a numeric vector, a single string, or a list-like object

When I checked the file for the fifth column, it is numeric as followed

peakIMR90MACS GRanges object with 41305 ranges and 7 metadata columns: seqnames ranges strand | NApeak1 X783 . X35.07343 <rle> <iranges> <rle> | <factor> <integer> <factor> <numeric> [1] chr1 10345-10464 * | NApeak2 245 . 14.3891 [2] chr1 27583-27667 * | NApeak3 22 . 3.59727 [3] chr1 28691-28734 * | NApeak4 22 . 3.59727 [4] chr1 28901-28944 * | NApeak5 53 . 5.39591 [5] chr1 29183-29299 * | NApeak6 53 . 5.39591 ... ... ... ... . ... ... ... ... [41301] chrY 58993885-58994018 * | NApeak41302 211 . 9.2396 [41302] chrY 58994906-58994963 * | NApeak41303 188 . 12.66612 [41303] chrY 58996504-58996620 * | NApeak41304 166 . 11.23844 [41304] chrY 58996926-58997039 * | NApeak41305 432 . 20.44031 [41305] chrY 58997239-58997319 * | NApeak41306 288 . 15.45911 X83.44460 X78.38238 X60 <numeric> <numeric> <integer> [1] 28.5818 24.5902 85 [2] 5.22289 2.26005 42 [3] 5.22289 2.26005 2 [4] 8.60475 5.31401 18 [5] 8.60475 5.31401 77 ... ... ... ... [41301] 25.04392 21.14383 88 [41302] 22.74032 18.89241 23 [41303] 20.42418 16.63574 82 [41304] 47.58882 43.22543 44 [41305] 32.98267 28.89663 38

I do not know why I am getting this error. Any help is appreciated.

Thanks in advance, Vasudha

chipseeker software error • 222 views
ADD COMMENTlink written 6 months ago by vasudha.sharma0

same here, got the same problem

ADD REPLYlink written 4 months ago by theodore.georgomanolis0
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