pruneSamples: Discarding samples

In larssnip/microRMS: Processing and analysis of RMS data

Discarding samples

Description

Discarding samples having too few reads mapped.

Usage

pruneSamples(rms.obj, mapping.threshold = 0, verbose = TRUE)

Arguments

rms.obj	A list with the tables Sample.tbl, see details below.
mapping.threshold	Minimum fraction of reads being mapped.
verbose	Turn on/off output text during processing (logical).

Details

The rms.obj must be a list with the required data structures. It must have a Sample.tbl, which is added to such an object with addSampleTable. It must also have a Readcount.mat, which is added by the readMapper.

The pruning means sample where the fraction of mapped reads to the total number of reads is below the threshold set by mapping.threshold. If very small fraction of reads are mapped, it probably indicates none of the genomes are present in the sample, and even if abundance estimates can be made they are also very unreliable in such cases.

Value

An RMS object where the Sample.tbl and Readcount.mat have been pruned, i.e. some samples have been discarded.

Author(s)

Lars Snipen.

See Also

RMSobject, readMapper, rmscols.

larssnip/microRMS documentation built on July 19, 2023, 1:06 a.m.