exomeCopy error in col name
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@chiararigobello-15139
Last seen 6.0 years ago

Hi , I'm having an error in exomeCopy when I computate fit.

(No previous error, following the vignette, and with provided data).

> fit <- exomeCopy(counts[seqnames(counts) ==
+ "chr1"], sample.name = "BIR", X.names = c("log.bg",
+ "GC", "GC.sq", "width"), S = 0:6, d = 2)
Error in exomeCopy(counts[seqnames(counts) == "chr1"], sample.name = "BIR",  :
  sample.name is not a column in rdata.

I've tried to check all objects containing name, but probably I've missed something!

 

any suggestion is appreciated

 

chiara

exomecopy • 745 views
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@mikelove
Last seen 18 hours ago
United States

Can you show that BIR is in fact a name in the mcols of the object? (That message is somewhat outdated because we no longer use RangedData but now GRanges.)

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I know that the problem is in that.

If I look at

colnames(mcols(counts))
 [1] "BIP"    "BIR"    "BIQ"    "AWI"    "AWJ"    "AWK"    "AWL"    "AWM"   
 [9] "BQ0"    "GC"     "GC.sq"  "bg"     "log.bg" "wdth"   "bg.var"

(That message is somewhat outdated because we no longer use RangedData but now GRanges.) --> how can I verified this?

Sorry, but I'm a self-taught in bioinformatics.

thanks for your help

 

 

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And are you using version 1.24 (the most recent version)?

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