importNgsLogs {ngsReports} | R Documentation |
Imports NGS-related log files such as those generated from stderr
importNgsLogs(x, type, which = 1)
x |
|
type |
|
which |
Which element of the parsed object to return. Ignored in all
file types except |
Imports one or more log files as output by tools such as:
bowtie
, bowtie2
, Hisat2
STAR
or
picard MarkDuplicates
A tibble
.
Column names are broadly similar to the text in supplied files,
but have been modified for easier handling under R naming conventions.
f <- c("bowtiePE.txt", "bowtieSE.txt") bowtieLogs <- system.file("extdata", f, package = "ngsReports") df <- importNgsLogs(bowtieLogs, type = "bowtie")