ExomeCNV - R - data.frame error

[sophiespo]

Hi,

I desperately need help.

I have created my coverage file using GATK like the ExomeCNV user guide says.

However when I use read.coverage.gatk("filename") in R, it throws this error:

Error in data.frame(probe = gatk$Target, chr = chr, probe_start = start, :
arguments imply differing number of rows: 235036, 235019, 1

The number of rows is definitely the first argument (23506) and not the second (23509) and I can't figure out where it is losing these rows.

Program works fine using the sample data on the ExomeCNV wiki.

I am quite new to R so maybe this problem has an easy fix - I just can't seem to find it!

Please help.

Thanks.

[bruce01]

Try looking at the file on the command line or in Excel if you are on Windows to see what the difference is, show the head and tail of the file here if you can't see it. You can just delete the rows not matching your probes, save and then read into R. Three extra lines may be resulting from header or such?

[sophiespo]

Thanks for replying. I think I have narrowed down the problem a little - though I am still not sure what is causing it.

I looked at the file in the command line and excel, looked at my interval file, they all match. They seem fine.

So I did:

head -1000 input.coverage > new.coverage

and then in R
read.coverage.gatk(new.coverage)

and it worked.

so then I did head -2000 and it gave a warning:
In matrix(as.integer(unlist(strsplit(chrpos[, 2], "-"))), ncol = 2, :
data length [3999] is not a sub-multiple or multiple of the number of rows [2000]

When I scroll up through the output I see this:

1998 chr1:13330308-13331001 chrchr1 13331001 13331242 242
1999 chr1:13331242-13331852 chrchr1 13331852 13351395 19544
2000 chr1:13351395-13351876 chrchr1 13351876 11943 -13339932

The value 11943 is coming up in the probe_end column for any length of file above about 1900 lines. Of course it is throwing it off. But I can't figure out WHY it is always putting 11943 in that column?

(I am sorry, I don't know how to show this as code)

Please help if anyone has any ideas??

UPDATE:

THANKYOU bruce01 - you have helped me solve my problem.

I just found that one of my lines looks like this:

chr1:11918179-11918777 30252 50.50 30252 50.50 18 38 87 76.6
chr1:11918785 17 17.00 17 17.00 18 18 18 100.0
chr1:11918787-11918928 3060 21.55 3060 21.55 16 20 32 79.6

I will edit and se how it goes.

[loga]

ExomeCNV error

Hi ,
I'm new to ExomeCNV. I have stuck up with the same issue. I deleted few of my rows as you did. But even then i'm getting the following error. Please let me know, how you sorted out this error. I'm new to R, and have no idea about R.


Error in data.frame(probe = gatk$Target, chr = chr, probe_start = start, :
arguments imply differing number of rows: 699, 627, 1
In addition: Warning message:
In matrix(as.integer(unlist(strsplit(chrpos[, 2], "-"))), ncol = 2, :
data length [1253] is not a sub-multiple or multiple of the number of rows [627]

[psyduck]

Hi ,
I'm new to ExomeCNV. I have stuck up with the same issue. I deleted few of my rows as you did. But even then i'm getting the following error. Please let me know, how you sorted out this error. I'm new to R, and have no idea about R.


Error in data.frame(probe = gatk$Target, chr = chr, probe_start = start, :
arguments imply differing number of rows: 699, 627, 1
In addition: Warning message:
In matrix(as.integer(unlist(strsplit(chrpos[, 2], "-"))), ncol = 2, :
data length [1253] is not a sub-multiple or multiple of the number of rows [627]

Hi,
I am also new to these, and have some problem, did you find a solution for this?
Best