extractFeature: Extract a specific feature/attribute of the sampleInfo...

In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given a sampleInfo object, the function extracts a defined feature(s) for given sample or sector.

Usage

extractFeature(sampleInfo, sector = NULL, samplename = NULL,
  feature = NULL)

Arguments

sampleInfo	sample information SimpleList object, which samples per sector/quadrant information along with other metadata.
sector	a vector or specific sector to extract the feature from. Default is NULL, which extracts all sectors.
samplename	a character vector or a specific sample to extract feature from. Default is NULL, which extracts all samples.
feature	Options include: primed, LTRed, linkered, decoded, and any of the metadata. Default is NULL. When feature='metadata', then it returns names of all the metadata elements associated with the sample as a comma separated list.

Value

a list or list of lists depending upon which parameters were supplied.

See Also

addFeature, findPrimers, findLTRs, findLinkers, extractSeqs, trimSeqs, getSectorsForSamples

Examples

load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
samples <- c('Roth-MLV3p-CD4TMLVWell6-Tsp509I', 
'Roth-MLV3p-CD4TMLVWell6-MseI', 'Roth-MLV3p-CD4TMLVwell5-MuA')
extractFeature(seqProps, sector='2', samplename=samples, feature="primed")
extractFeature(seqProps, sector='2', samplename=samples, feature="linkered")
extractFeature(seqProps, sector='2', samplename=samples, feature="metadata")

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.