Question: exomeCopy compileCopyCountSegments error
0
4 months ago by
kkyung4120 wrote:

Hello.

I am getting an error message with the exomecopy, compileCopyCountSegments

compileCopyCountSegments(fit.list)

Error in FUN(X[[i]], ...) :

trying to get slot "path" from an object of a basic class ("NULL") with no slots

When I looked at the Fit.list, there was really NULL data How can I handle this?

[[3]][[16]] NULL

[[3]][[17]] NULL

[[3]][[18]] NULL

[[3]][[19]] NULL

[[3]][[20]] NULL

[[3]][[21]] NULL

[[3]][[22]] NULL

[[3]][[23]] NULL

[[3]][[24]] NULL

exomecopy • 80 views
modified 4 months ago by Michael Love26k • written 4 months ago by kkyung4120
0
4 months ago by
Michael Love26k
United States
Michael Love26k wrote:

I haven't touched exomeCopy in years, maybe since 2011, so I don't remember the details. Perhaps there are no calls in fit.list? Can you plot one of the fits to see if there are any calls outside of copy number = 2?

hi Michael

I can't draw a plot now. The warning message for exomeCopy was as follows. Please help me.ㅜㅜ

1: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 2: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 3: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 4: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 5: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 6: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 7: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 8: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL 9: In exomeCopy(counts[seqnames(counts) == seq.name], sample.name, : More than 90% of sample counts are zero, exomeCopy will return NULL

It looks like the reason it returns NULL is because there are many 0’s.

It looks like the reason it returns NULL is because there are many 0’s.

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