alignSummarySTAR: Extracts the alignment summary from STAR log files.
In steveped/NGS2R: Provides access to some common NGS log files from within R

Description Usage Arguments Details Value Author(s)

Extracts the basic summary for fastq files after running fastqc.

1	readSTARLogs(logFiles, logPath, pattern = "Log.final.out")

`logFiles`	A `vector` of log files. Any files which cannot be found will be ignored. If `logPath` is not specified, these must contain path information as part of each filename
`logPath`	The path to the directory where the log files are located. If no files are specified, this will default to all files which match the pattern "Log.out"
`pattern`	A text string found in the name of all required logFiles. Not used if the files are specified by name.

This will open the log files as output by the alignment tool STAR and load the information into your workspace. The log files in question are the ones traditionally output with the suffix "Log.final.out"

a list with components $reads, $splicing, $lengths, $indels and $performance. Each of thsi will be a data.frame with samples as rows and the key information as columns.

Steve Pederson <stephen.pederson@adelaide.edu.au>

steveped/NGS2R documentation built on May 30, 2019, 5:38 p.m.