chromoMap Error: .rowNamesDF<-`(x, value = value) : invalid 'row.names' length

Question

[kamanovae]

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) :

[gubrins]

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:

chr1    1   1000
chr2    1   700

and as annotation_pos:

An1 chr1    558 560
An2 chr2    396 398

I hope it helps!

[Jocelyn]

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.

Answer 1

[Alice]

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
...