summaryTable: Summary and count table of shRNA by sample
In genialis/shRNAde: Functions needed to support the shRNA pipeline in rewolwe-bio

Produce a summary report. Report will include data for total number of reads, 5' trimmed reads, 3' trimmed reads, number and percent of mapped reads, number and percent of perfectly mapped reads, number and percent of good mapped reads, number and percent of poorly mapped reads and number of unmapped reads.

summaryTable(samkey, lib, trimreport, mapping_path = ".",
  mapping_rx = "^.*_mapped_species\\.txt$", wt_alignscores = 0,
  wt_readlengths_lower = 26, high_alignscores_upper = 0,
  high_alignscores_lower = -6, high_readlengths_lower = 26,
  low_alignscores_upper = -6, low_readlengths_upper = 26,
  count_alignscores = -6, count_readlengths = 26,
  output_report = "global_alignment_report.txt",
  output_count = "count_matrix.txt")

`samkey`	Character. A link to sample key file. See source code for how the data should be structured.
`lib`	Character. A link to library (fasta) file. See source code for how the data should be structured.
`trimreport`	Character. A link to global trim report from the pipeline. See source code for how the data should be structured.
`mapping_path`	Character. Path to where mapping files reside.
`mapping_rx`	Character. Valid regular expression for collating of mapping files (per sample).
`wt_alignscores`	Integer. Perfect align counts. Align counts that have align scores equal to `wt_alignscores` and read lengths equal or higher to `wt_readlengths_lower` will be summed.
`wt_readlengths_lower`	Integer. Perfect align counts. Align counts that have align scores equal to `wt_alignscores` and read lengths equal or higher to `wt_readlengths_lower` will be summed.
`high_alignscores_lower, high_alignscores_upper, high_readlengths_lower`	Integer. Good align counts. Align counts with align scores >= `high_alignscores_lower` and < `high_alignscores_upper` and read lengths equal or higher than `high_readlengths_lower` will be summed.
`low_alignscores_upper, low_readlengths_upper`	Integer. Poor align counts. Align counts below `low_alignscores_upper` or read length below `low_readlengths_upper` will be excluded from the tally.
`count_alignscores, count_readlengths`	Integer. For count matrix, align counts for which align scores equal or greater to `count_alignscores` and read lengths equal or greater to `count_readlengths` will be used in the final tally.
`output_report`	Character. A name of file (incl. file extension) into which alignment report will be written to.
`output_count`	Character. A name of file (incl. file extension) into which count matrix (shRNA for rows, sample names for columns) will be written.

Two files, global_alignment_report.txt and count_matrix.txt are written as a side effect. Function returns a list of length 2 where one can access alignment report (output$alignment_report) or count matrix (output$count_matrix).

genialis/shRNAde documentation built on Dec. 11, 2018, 1:34 a.m.