Description Usage Arguments Value
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.
1 2 3 4 5 6 7 8 | summaryTable(samkey, lib, trimreport, mapping_path = ".",
mapping_rx = "^.*_mapped_species\\.txt$", wt_alignscores = 0,
wt_readlengths_lower = 26, high_alignscores_upper = 0,
high_alignscores_lower = -6, high_readlengths_lower = 26,
low_alignscores_upper = -6, low_readlengths_upper = 26,
count_alignscores = -6, count_readlengths = 26,
output_report = "global_alignment_report.txt",
output_count = "count_matrix.txt")
|
samkey |
Character. A link to sample key file. See source code for how the data should be structured. |
lib |
Character. A link to library (fasta) file. See source code for how the data should be structured. |
trimreport |
Character. A link to global trim report from the pipeline. See source code for how the data should be structured. |
mapping_path |
Character. Path to where mapping files reside. |
mapping_rx |
Character. Valid regular expression for collating of mapping files (per sample). |
wt_alignscores |
Integer. Perfect align counts. Align counts that have align scores equal to |
wt_readlengths_lower |
Integer. Perfect align counts. Align counts that have align scores equal to |
high_alignscores_lower, high_alignscores_upper, high_readlengths_lower |
Integer. Good align counts. Align counts with align
scores >= |
low_alignscores_upper, low_readlengths_upper |
Integer. Poor align counts. Align counts below |
count_alignscores, count_readlengths |
Integer. For count matrix, align counts for which align scores equal or greater to
|
output_report |
Character. A name of file (incl. file extension) into which alignment report will be written to. |
output_count |
Character. A name of file (incl. file extension) into which count matrix (shRNA for rows, sample names for columns) will be written. |
Two files, global_alignment_report.txt
and count_matrix.txt
are written as a side effect. Function
returns a list of length 2 where one can access alignment report (output$alignment_report
) or count matrix
(output$count_matrix
).
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