[Bioc-sig-seq] perTile QA element in the FastqQA class

[Sirisha Sunkara]

Hi Martin,

The qa function that reads in fastq format files, doesn't seem to 
populate the perTile QA element with row information...
The row counts are zero for both the readCounts and 
medianReadQualityScore list elements of perTile.

Is this feature still work in progress..? Essentially, I am trying to 
get the TileQC plots for lanes where there was no reference genome to 
align (no export.txt files)

 >  qafq <- qa("./Contam_Screening/Run703/","s_8_1_sequence.txt", 
type="fastq")
 > qafq
class: FastqQA(9)
QA elements (access with qa[["elt"]]):
  readCounts: data.frame(1 3)
  baseCalls: data.frame(1 5)
  readQualityScore: data.frame(512 4)
  baseQuality: data.frame(94 3)
  alignQuality: data.frame(1 3)
  frequentSequences: data.frame(50 4)
  sequenceDistribution: data.frame(1663 4)
  perCycle: list(2)
    baseCall: data.frame(150 4)
    quality: data.frame(1081 5)
  perTile: list(2)
    readCounts: data.frame(0 4)
    medianReadQualityScore: data.frame(0 4)

Thank You,
Sirisha

 > sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-07 r51225)
x86_64-unknown-linux-gnu

locale:
[1] C

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

other attached packages:
[1] ShortRead_1.5.21    lattice_0.18-3      Biostrings_2.15.22
[4] GenomicRanges_0.1.0 IRanges_1.5.74      Rmpi_0.5-8        

loaded via a namespace (and not attached):
[1] Biobase_2.7.5 grid_2.11.0   hwriter_1.2   tools_2.11.0