chromoMap Error: .rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Hi!
I am trying to run the program chromoMap. But I am getting the error:
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
My program start looks like this:
library(chromoMap)
chr_file_1 =read.table("~/chr_file.txt",sep = "\t", quote="", stringsAsFactors=FALSE)
print(chr_file_1)
annot_file_1= read.table("~/annotation_pos.txt",sep = "\t",quote="", stringsAsFactors=FALSE)
print(annot_file_1)
chromoMap( "chr_file.txt", "annotation_pos.txt")
All input files were generated based on the instruction
chr_file.txt:
V1 V2 V3
1 chr1 332315086 32400268
annot_file_1:
V1 V2 V3 V4 V5
1 rs144848 chr13 32906729 32906729 c.1114A>C
2 rs169547 chr13 32929387 32929387 c.7397T>C
3 rs11571833 chr13 32972626 32972626 c.9976A>T
If I run the function differently, then I get a new error
chromoMap(chr_file_1, annot_file_1)
Error: The number of data files(s) must same as the number of chromsome file(s) Error in chromoMap(chr_file_1, annot_file_1) :
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Alice •
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kamanovae •
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kamanovae •
1 answer
Hi ! I don't know if you managed at the end, and hope it can help someone else : by using lists, it gave me the map, while I get the same error as you if I don't:
chromoMap(list(chr_file_1),list(annot_file_1))
chromoMap(chr_file_1, annot_file_1)
Error: The number of data files(s) must same as the number of chromsome file(s)
Error in chromoMap(chromSize, test) :
Here are how look my two dataframes (might be a matter of class): chr_file_1
V1 V2 V3
1 1 1 6088797
2 2 1 3860111
...
annot_file_1
V1 V2 V3 V4
1 ZtIPO323_1_GATC_1 1 572 576
2 ZtIPO323_1_GATC_2 1 758 762
...
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Heys! Did you solve it? I also had a lot of issues because of formatting. Could be that the annot_file_1 is not separated by tabs? Just in case I leave here these two files that work for me:
as chr_file_1:
and as annotation_pos:
I hope it helps!
In "chr_file.txt" you have chr1 listed, no chr13. In "annot_file_1.txt" you have chr13 listed, no chr1.
I wonder if this may have something to do with the error?
I am having the same issue, but with loading data.frames not files, and seeing this makes me wonder if the extraneous chromosome information I have in my chr_file.txt may be the issue.