isoSelect: Method to select specific miRNAs from an IsomirDataSeq...

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Method to select specific miRNAs from an IsomirDataSeq object.

Description

This method allows to select a miRNA and all its isomiRs from the count matrix.

Usage

isoSelect.IsomirDataSeq(object, mirna, minc = 10)

## S4 method for signature 'IsomirDataSeq'
isoSelect(object, mirna, minc = 10)

Arguments

object	A IsomirDataSeq object.
mirna	String referring to the miRNA to show.
minc	Minimum number of isomiR reads needed to be included in the table.

Value

S4Vectors::DataFrame with count information. The row.names show the isomiR names, and each of the columns shows the counts for this isomiR in that sample. Mainly, it will return the count matrix only for isomiRs belonging to the miRNA family given by the mirna parameter. IsomiRs need to have counts bigger than minc parameter at least in one sample to be included in the output. Annotation of isomiRs follows these rules:

• miRNA name

• mismatches

• additions

• 5 trimming events

• 3 trimming events

Author(s)

Lorena Pantano

Examples

data(mirData)
# To select isomiRs from let-7a-5p miRNA
# and with 10000 reads or more.
isoSelect(mirData, mirna="hsa-let-7a-5p", minc=10000)

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.