summariseFilteringStats: Collects summary statistics on filtering This function...

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

Collects summary statistics on filtering This function collects summary stats from the filterBadSeqs function, and prints out data to a PDF. Two graphs are output. In the first, the data shows, for each fastq read file, how many reads went in, how many went out, and the mean and median sizes of the output fastq files. The second shows the proportion of reads trimmed or removed for each fastq file.

Usage

summariseFilteringStats(x)

Arguments

x	A dataframe returned from filterBadSeqs).

Value

A dataframe. The dataframe contains the number of reads which have been trimmed (on leading or trailing tails) for poor quality or unknown bases, the number of reads which have been removed entirely due to poor quality, possession of unknown bases, or length too short. Also produces graphs of absolute number of reads output, and relative numbers of reads which have been trimmed or removed (in PDF format).

See Also

filterBadSeqs

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.