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                  

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>