DMRcate error in extractCoords function
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Entering edit mode
@xavier-pastor-7554
Last seen 3.2 years ago
Germany

Hi,

When running the extractRanges function from the DMRcate package on a dmrcate.output object reporting only one DMR I get the following error:

Error in `$<-.data.frame`(`*tmp*`, "chromStart", value = integer(0)) :
  replacement has 0 rows, data has 3

It seems to me that in such case the function extractCoords doesn't report a data frame with coordinates, as it should, but a character vector instead.

What about something like?:

extractCoords <- function(xx)
{
  coords <- sapply(xx, strsplit, '[:-]')
  coords <- as.data.frame(do.call(rbind, coords), stringsAsFactors=F)
  colnames(coords) <- c('chrom', 'chromStart', 'chromEnd')
  return(coords)
}

Is it a valid solution?

 

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)

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] splines   grid      parallel  stats4    stats     graphics  grDevices
 [8] utils     datasets  methods   base     

other attached packages:
 [1] DMRcate_1.10.1             DMRcatedata_1.10.1        
 [3] DSS_2.14.0                 bsseq_1.10.0              
 [5] minfi_1.20.0               bumphunter_1.14.0         
 [7] locfit_1.5-9.1             iterators_1.0.8           
 [9] foreach_1.4.3              Biostrings_2.42.0         
[11] XVector_0.14.0             SummarizedExperiment_1.4.0
[13] Biobase_2.34.0             ComplexHeatmap_1.12.0     
[15] gridExtra_2.2.1            limma_3.30.6              
[17] ggplot2_2.2.0              GenomicRanges_1.26.1      
[19] GenomeInfoDb_1.10.0        IRanges_2.8.0             
[21] S4Vectors_0.12.0           BiocGenerics_0.20.0

 

Thanks,
Xavier

software error DMRcate extractRanges • 506 views
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Entering edit mode
Tim Peters ▴ 120
@tim-peters-7579
Last seen 6 weeks ago
Australia

Hi Xavier,

Yes, that's exactly what it should be. Thank you. Git and svn are now patched with acknowledgements. 

Cheers,

Tim

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0
Entering edit mode

Hi Tim,

Thanks a lot :-),

Xavier

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