aggregate_fqc: Aggregate and summarise FastQC reports for multiple samples

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

Aggregate and summarise multiple FastQC reports.

Usage

aggregate_fqc(object)

module_fqc(object)

stats_fqc(object)

Arguments

object

A fqcRes.multi object produced by 'read_multifastqc()'.

Value

• aggregate_fqc() returns a list containing two data-frames. The first data-frame has the following columns:

  • sample: sample names

  • tot.seq: total sequences (i.e.: the number of reads)

  • low.qual: the number of sequences flagged as poor quality

  • seq.len: sequence length

  • pct.gc: % of GC content

  • pct.dup: % of duplicate reads

  In the second datframe, each row is a sample and the columns are the FASTQC modules. Each cell indicates the outcome (pass, warn or fail) for that module by each sample.

• module_fqc(): Generates a list of summarising the module results.

  • The first list item is a dataframe, in which each row is a sample and the columns are the FASTQC modules. Each cell indicates the outcome (pass, warn or fail) for that module by each sample.

  • The second item summarises the module results per module, indicating for each module, how many samples passed, warned or failed. In addition, individual summaries for warned and failed are provided.

  • The third item summrises the module results per sample, indicating for each sample, how many modules passed, warned or failed. In addition, individual summaries for warned and failed are provided.

• stats_fqc(): returns a data frame containing basic metrics of the fastqc reports. Columns are: sample, tot.seq, low.qual.seq, seq.len, pct.gc, and pct.dup.

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.