qaFilter: Quality filter a brentlabRnaSeqSet object

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

Quality filter a brentlabRnaSeqSet object

Description

Filter for manual passes (overrides auto fail), automatic passes (unless auto failed), and optionally RLE IQR

Filter for manual passes (overrides auto fail), automatic passes (unless auto failed), and optionally RLE IQR

Usage

qaFilter(x, ...)

## S4 method for signature 'brentlabRnaSeqSet'
qaFilter(x)

## S4 method for signature 'brentlabRnaSeqExperiment'
qaFilter(x, rle_iqr_threshold = NA, iqr_colname = NA)

Arguments

x	a brentlabRnaSeqSet object
...	other arguments
rle_iqr_threshold	default is NA, which means no rle_iqr_threshold filtering. Set a value to filter based on RLE IQR. Note: RLE stats are all calculated after removing the libraryDate effect.
iqr_colname	default is NA, which creates the iqr col name from the set name in the object. Pass the col name itself, eg "my_set_iqr", to specify a iqr column name manually

Value

a quality assessment filtered brentlabRnaSeqSet object

a quality assessment filtered brentlabRnaSeqExperiment object

Note

on the brentlabRnaSeqSet (as opposed to the brentlabRnaSeqExperiment), this only filters on manualAudit and autoAudit. no rle filtering

If there are less than 3 replicates, the RLE stats will be NA. These are returned, also. Filter them out of the returned object if you wish to have only those samples with more than 3 replicates.

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.