derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
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Entering edit mode
Wayne • 0
@wayne-12952
Last seen 7.2 years ago

Hi,

I am trying to use derfinder to analyze samples from Saccharomyces cerevisiae. I am able to supply the species and chromosome style information in the `fullCoverage()` command, but when I go to do `regionMatrix()` the style has changed.

This is my code to get to the `fullCoverage()` call:

##Load libraries
library('derfinder')
library('GenomicRanges')
file_designations <- c("WT1","WT2","WT3", "MT1", "MT2", "MT3")
chrs_all = c('I', 'II','III','IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'MT')
## Load the data from disk
files <- file.path("/data/alignments", file_designations , paste0(file_designations,"Aligned.sorted.bam"))
system.time(fullCov <- fullCoverage(files = files, chrs = chrs_all,
    totalMapped = sapply(files,getTotalMapped, chrs = chrs_all), targetSize = 8e+07, species = "Saccharomyces_cerevisiae",currentStyle = 'NCBI'))   

That worked and I'll include some fragments of it so you can see the chromosome names:

2017-05-08 17:10:19 fullCoverage: processing chromosome I
2017-05-08 17:10:19 loadCoverage: finding chromosome lengths
...
2017-05-08 17:10:23 loadCoverage: applying the cutoff to the merged data
2017-05-08 17:10:23 filterData: normalizing coverage
2017-05-08 17:10:24 filterData: done normalizing coverage
2017-05-08 17:10:24 filterData: originally there were 230218 rows, now there are 230218 rows. Meaning that 0 percent was filtered.
2017-05-08 17:10:24 fullCoverage: processing chromosome II
2017-05-08 17:10:24 loadCoverage: finding chromosome lengths
...
2017-05-08 17:10:44 loadCoverage: applying the cutoff to the merged data
2017-05-08 17:10:44 filterData: normalizing coverage
2017-05-08 17:10:44 filterData: done normalizing coverage
2017-05-08 17:10:44 filterData: originally there were 813184 rows, now there are 813184 rows. Meaning that 0 percent was filtered.
2017-05-08 17:10:44 fullCoverage: processing chromosome III
2017-05-08 17:10:44 loadCoverage: finding chromosome lengths
...

Next I want to run the `regionMatrix()` command. After seeing Leonardo's reply to my other post -> (C: regionMatrix for derfinder crashes with seqnames issue on non-human data) , I gave the style to the `regionMatrix()` command too.

system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, species = "Saccharomyces_cerevisiae", currentStyle = 'NCBI'))

Unexpectedly, that encountered an error in the first chromosome it tried:

    > system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, species = "Saccharomyces_cerevisiae", currentStyle = 'NCBI'))
    2017-05-08 17:28:10 regionMatrix: processing chrI
    2017-05-08 17:28:10 filterData: originally there were 230218 rows, now there are 174908 rows. Meaning that 24.03 percent was filtered.
    2017-05-08 17:28:10 findRegions: identifying potential segments
    2017-05-08 17:28:10 findRegions: segmenting information
    2017-05-08 17:28:10 findRegions: identifying candidate regions
    Error in validObject(.Object) : 
      invalid class “GRanges” object: 'seqnames(x)' contains missing values
    Timing stopped at: 0.308 0 0.311 

So I tried without the species and chromosome style and that worked. Curiously, though, I saw that the chromosome style was now different.

> system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75))
2017-05-08 17:29:23 regionMatrix: processing chrI
2017-05-08 17:29:23 filterData: originally there were 230218 rows, now there are 174908 rows. Meaning that 24.03 percent was filtered.
2017-05-08 17:29:23 findRegions: identifying potential segments
2017-05-08 17:29:23 findRegions: segmenting information
2017-05-08 17:29:23 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:29:23 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:29:23 getRegionCoverage: processing chrI
2017-05-08 17:29:23 getRegionCoverage: done processing chrI
2017-05-08 17:29:23 regionMatrix: calculating coverageMatrix
2017-05-08 17:29:24 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-08 17:29:24 regionMatrix: processing chrII
2017-05-08 17:29:25 filterData: originally there were 813184 rows, now there are 670986 rows. Meaning that 17.49 percent was filtered.
2017-05-08 17:29:25 findRegions: identifying potential segments
2017-05-08 17:29:25 findRegions: segmenting information
2017-05-08 17:29:25 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:29:25 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:29:25 getRegionCoverage: processing chrII
...

Okay. Now I see from my table here -> (C: regionMatrix for derfinder crashes with seqnames issue on non-human data) that the chromosomes are in the UCSC format. They changed. Thus, I assume I should be able to add the chromosome style as UCSC in the `regionMatrix()` call and I'll cease to see `extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.`.

But that is not the case. I still see `extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.`

> system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, species = "Saccharomyces_cerevisiae", currentStyle = 'UCSC'))
2017-05-08 17:37:06 regionMatrix: processing chrI
2017-05-08 17:37:07 filterData: originally there were 230218 rows, now there are 174908 rows. Meaning that 24.03 percent was filtered.
2017-05-08 17:37:07 findRegions: identifying potential segments
2017-05-08 17:37:07 findRegions: segmenting information
2017-05-08 17:37:07 findRegions: identifying candidate regions
2017-05-08 17:37:07 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:37:07 getRegionCoverage: processing chrI
2017-05-08 17:37:07 getRegionCoverage: done processing chrI
2017-05-08 17:37:07 regionMatrix: calculating coverageMatrix
2017-05-08 17:37:07 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-08 17:37:07 regionMatrix: processing chrII
2017-05-08 17:37:08 filterData: originally there were 813184 rows, now there are 670986 rows. Meaning that 17.49 percent was filtered.
2017-05-08 17:37:08 findRegions: identifying potential segments
2017-05-08 17:37:08 findRegions: segmenting information
2017-05-08 17:37:08 findRegions: identifying candidate regions
2017-05-08 17:37:08 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-08 17:37:08 getRegionCoverage: processing chrII
...

I even tried `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, species = "Saccharomyces_cerevisiae", chrsStyle = 'UCSC'))
` after seeing Leonardo's reply here -->(C: regionMatrix for derfinder crashes with seqnames issue on non-human data). I still get the same thing about the style. Same for `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, currentStyle = 'UCSC'))` and `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, chrsStyle = 'UCSC'))` and `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75))`. I even tried `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75, chrsStyle = 'NULL'))` after seeing Leonarado's reply here ---> (C: regionMatrix for derfinder crashes with seqnames issue on non-human data). Still see `extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.`

First, is `fullCoverage()` supposed to switch the style? Fine, if so. However, it would be helpful to know how to write the `regionMatrix()` call subsequently? Am I doing something wrong or maybe the code is overlooking what I supplied in `currentStyle` in the `regionMatrix()` call ? Everything seems to work despite that curious message.

 

> session_info()
Session info -----
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       <NA>                        
 date     2017-05-08                  

Packages ------
 package              * version  date       source        
 acepack                1.4.1    2016-10-29 CRAN (R 3.3.1)
 AnnotationDbi          1.36.2   2017-03-10 Bioconductor  
 backports              1.0.5    2017-01-18 CRAN (R 3.3.1)
 base64enc              0.1-3    2015-07-28 CRAN (R 3.3.1)
 Biobase                2.34.0   2017-03-10 Bioconductor  
 BiocGenerics         * 0.20.0   2017-03-10 Bioconductor  
 BiocParallel           1.8.2    2017-05-01 Bioconductor  
 biomaRt                2.30.0   2017-03-10 Bioconductor  
 Biostrings             2.42.1   2017-03-10 Bioconductor  
 bitops                 1.0-6    2013-08-17 CRAN (R 3.3.1)
 BSgenome               1.42.0   2017-03-10 Bioconductor  
 bumphunter             1.14.0   2017-05-01 Bioconductor  
 checkmate              1.8.2    2016-11-02 CRAN (R 3.3.1)
 cluster                2.0.6    2017-03-16 CRAN (R 3.3.1)
 codetools              0.2-15   2016-10-05 CRAN (R 3.3.1)
 colorspace             1.3-2    2016-12-14 CRAN (R 3.3.1)
 data.table             1.10.4   2017-02-01 CRAN (R 3.3.1)
 DBI                    0.6-1    2017-04-01 CRAN (R 3.3.1)
 derfinder            * 1.8.5    2017-05-01 Bioconductor  
 derfinderHelper        1.8.1    2017-05-01 Bioconductor  
 devtools             * 1.12.0   2016-12-05 CRAN (R 3.3.1)
 digest                 0.6.12   2017-01-27 CRAN (R 3.3.1)
 doRNG                  1.6.6    2017-04-10 CRAN (R 3.3.1)
 foreach                1.4.3    2015-10-13 CRAN (R 3.3.1)
 foreign                0.8-68   2017-04-24 CRAN (R 3.3.1)
 Formula                1.2-1    2015-04-07 CRAN (R 3.3.1)
 GenomeInfoDb         * 1.10.3   2017-03-10 Bioconductor  
 GenomicAlignments      1.10.1   2017-05-01 Bioconductor  
 GenomicFeatures        1.26.4   2017-05-01 Bioconductor  
 GenomicFiles           1.10.3   2017-05-01 Bioconductor  
 GenomicRanges        * 1.26.4   2017-05-01 Bioconductor  
 ggplot2                2.2.1    2016-12-30 CRAN (R 3.3.1)
 gridExtra              2.2.1    2016-02-29 CRAN (R 3.3.1)
 gtable                 0.2.0    2016-02-26 CRAN (R 3.3.1)
 Hmisc                  4.0-2    2016-12-31 CRAN (R 3.3.1)
 htmlTable              1.9      2017-01-26 CRAN (R 3.3.1)
 htmltools              0.3.6    2017-04-28 CRAN (R 3.3.1)
 htmlwidgets            0.8      2016-11-09 CRAN (R 3.3.1)
 IRanges              * 2.8.2    2017-05-01 Bioconductor  
 iterators              1.0.8    2015-10-13 CRAN (R 3.3.1)
 knitr                  1.15.1   2016-11-22 CRAN (R 3.3.1)
 lattice                0.20-35  2017-03-25 CRAN (R 3.3.1)
 latticeExtra           0.6-28   2016-02-09 CRAN (R 3.3.1)
 lazyeval               0.2.0    2016-06-12 CRAN (R 3.3.1)
 locfit                 1.5-9.1  2013-04-20 CRAN (R 3.3.1)
 magrittr               1.5      2014-11-22 CRAN (R 3.3.1)
 Matrix                 1.2-10   2017-04-28 CRAN (R 3.3.1)
 matrixStats            0.52.2   2017-04-14 CRAN (R 3.3.1)
 memoise                1.1.0    2017-04-21 CRAN (R 3.3.1)
 munsell                0.4.3    2016-02-13 CRAN (R 3.3.1)
 nnet                   7.3-12   2016-02-02 CRAN (R 3.3.1)
 pkgmaker               0.22     2014-05-14 CRAN (R 3.3.1)
 plyr                   1.8.4    2016-06-08 CRAN (R 3.3.1)
 qvalue                 2.6.0    2017-05-01 Bioconductor  
 RColorBrewer           1.1-2    2014-12-07 CRAN (R 3.3.1)
 Rcpp                   0.12.10  2017-03-19 CRAN (R 3.3.1)
 RCurl                  1.95-4.8 2016-03-01 CRAN (R 3.3.1)
 registry               0.3      2015-07-08 CRAN (R 3.3.1)
 reshape2               1.4.2    2016-10-22 CRAN (R 3.3.1)
 rngtools               1.2.4    2014-03-06 CRAN (R 3.3.1)
 rpart                  4.1-11   2017-04-21 CRAN (R 3.3.1)
 Rsamtools              1.26.2   2017-05-01 Bioconductor  
 RSQLite                1.1-2    2017-01-08 CRAN (R 3.3.1)
 rtracklayer            1.34.2   2017-03-10 Bioconductor  
 S4Vectors            * 0.12.2   2017-05-01 Bioconductor  
 scales                 0.4.1    2016-11-09 CRAN (R 3.3.1)
 stringi                1.1.5    2017-04-07 CRAN (R 3.3.1)
 stringr                1.2.0    2017-02-18 CRAN (R 3.3.1)
 SummarizedExperiment   1.4.0    2017-03-10 Bioconductor  
 survival               2.41-3   2017-04-04 CRAN (R 3.3.1)
 tibble                 1.3.0    2017-04-01 CRAN (R 3.3.1)
 VariantAnnotation      1.20.3   2017-05-01 Bioconductor  
 withr                  1.0.2    2016-06-20 CRAN (R 3.3.1)
 XML                    3.98-1.6 2017-03-30 CRAN (R 3.3.1)
 xtable                 1.8-2    2016-02-05 CRAN (R 3.3.1)
 XVector                0.14.1   2017-05-01 Bioconductor  
 zlibbioc               1.20.0   2017-03-10 Bioconductor  
> 

 

derfinder • 1.3k views
ADD COMMENT
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Entering edit mode

Hi Wayne,

Can you post the output of:

names(fullCov)

after you created it with:

fullCov <- fullCoverage(files = files, chrs = chrs_all,
    totalMapped = sapply(files,getTotalMapped, chrs = chrs_all), targetSize = 8e+07, species = "Saccharomyces_cerevisiae",currentStyle = 'NCBI')

Also, are the chromosome names in UCSC or NCBI style in your bam files?

I have a pretty good idea of what is going on, but it could be that you don't need all the complicated chromosome name changes.

Thanks!

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