importNgsLogs {ngsReports}R Documentation

Import Various NGS-related log files

Description

Imports NGS-related log files such as those generated from stderr

Usage

importNgsLogs(x, type, which = 1)

Arguments

x

character. Vector of filenames. All log files must be of the same type. Duplicate file paths will be silently ignored.

type

character. The type of file being imported. Can be one of bowtie, bowtie2, hisat2, star or duplicationMetrics

which

Which element of the parsed object to return. Ignored in all file types except type = "duplicationMetrics", which can return either the metrics or the data supplied as a histogram. Defaults to the metrics data.

Details

Imports one or more log files as output by tools such as: bowtie, bowtie2, Hisat2 STAR or picard MarkDuplicates

Value

A tibble. Column names are broadly similar to the text in supplied files, but have been modified for easier handling under R naming conventions.

Examples

f <- c("bowtiePE.txt", "bowtieSE.txt")
bowtieLogs <- system.file("extdata", f, package = "ngsReports")
df <- importNgsLogs(bowtieLogs, type = "bowtie")


[Package ngsReports version 1.0.1 Index]