[Bioc-devel] Inconsistent behaviour in ShortRead::nFilter()

[Anita Lerch]

Hi,
I found an inconsistent behaviour in the ShortRead::nFilter() function.
The column name for the results of evalSeparately() differ (CleanNFilter
vs CleanNFilter.other) if there is only one sequence in the ShortRead
object.

Here an example for reproducing this behaviour:

> library(ShortRead)
> nFilt <- nFilter(10)
> filters <- c(nFilt)
> reads2 <- ShortRead(sread=c(DNAStringSet("CGATTGGCGCGGATTCCGACCAAACAGATCGGAAG"),
+                             DNAStringSet("CGATTGGCGCGGATTCCGACCAAACAGATCGGAAG")))
> res2 <- evalSeparately(filters, reads2)
> res2
     CleanNFilter
[1,]         TRUE
[2,]         TRUE


> reads1 <- ShortRead(sread=DNAStringSet("CGATTGGCGCGGATTCCGACCAAACAGATCGGAAG"))
> res1 <- evalSeparately(filters, reads1)
> res1
CleanNFilter.other 
              TRUE 
> class(res2)
[1] "matrix"
> class(res1)
[1] "logical"

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ShortRead_1.12.2    latticeExtra_0.6-19 RColorBrewer_1.0-5  Rsamtools_1.6.2     lattice_0.19-33     Biostrings_2.22.0  
[7] GenomicRanges_1.6.4 IRanges_1.12.4     

loaded via a namespace (and not attached):
 [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    grid_2.14.0        hwriter_1.3        RCurl_1.8-0       
 [7] rtracklayer_1.14.4 tools_2.14.0       XML_3.6-1          zlibbioc_1.0.0

Greetings
Anita
 
-- 
Anita Lerch
Friedrich Miescher Institute
Maulbeerstrasse 66
WRO-1066.P22
4058 Basel
Phone: +41 (0)61 697 5172
Email: anita.lerch at fmi.ch