OmicCircos Error in Colnames attribute mus be the same length as the vector
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theobroma22 ▴ 10
@theobroma22-11920
Last seen 4.7 years ago

Dear Ying,

I have my data.frame of 'karyotype' chromosomes:

> par.chr
   seg.name seg.Start   seg.End
1      mdm1         1  29289779
2      mdm2  29289779  65664585
3      mdm3  65664585  99375387
4      mdm4  99375387 122396126
5      mdm5 122396126 154003081
6      mdm6 154003081 179476216
7      mdm7 179476216 205859750
8      mdm8 205859750 235463689
9      mdm9 235463689 269181364
10    mdm10 269181364 302572599
11    mdm11 302572599 337872134
12    mdm12 337872134 369550824
13    mdm13 369550824 404269910
14    mdm14 404269910 433428769
15    mdm15 433428769 480609771
16    mdm16 480609771 501274164
17    mdm17 501274164 526197889

However, when I try to convert to the angle values I get the following error. I tried changing the colnames to c("chr", "seg.start", "seg.end") <- as shown in the ref. manual but I get the same error. I'm only using the three required columns, so I don't have the optional columns 4 and 5.

    pchrs <- segAnglePo(seg.dat = par.chr, seg = seg.name)
    Error in `colnames<-`(`*tmp*`, value = c("seg.name", "seg.Start", "seg.End",  :
    'names' attribute [5] must be the same length as the vector [3]

I also tried changing the seg.name names:

    n <- 17
    m <- paste("chr", 1:n, sep="")
    m
    [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"
    [10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"                                                   

    par.chr$seg.name <- m

    head(par.chr)
    seg.name seg.Start   seg.End

    1     chr1         1  29289779
    2     chr2  29289779  65664585
    3     chr3  65664585  99375387
    4     chr4  99375387 122396126
    5     chr5 122396126 154003081
    6     chr6 154003081 179476216

    pchrs <- segAnglePo(seg.dat = par.chr, seg = seg.name)

    > attributes(par.chr)
    $names
    [1] "seg.name"  "seg.Start" "seg.End"  

    $class
    [1] "data.frame"

    $row.names
     [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17

I also looked this error up on stackoverflow and biostars. A workaround was to install a previous package version. Such was the case with dplyr 1.7. However, I wanted to contact you to ask you if I should install a previous version, the current developers version or if there is another way using the current package.

Thanks,

Franklin 

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] OmicCircos_1.8.1     GenomicRanges_1.22.4 GenomeInfoDb_1.6.3  
[4] IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 tools_3.2.3     XVector_0.10.0

 

 

 

r omiccircos • 753 views
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