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

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

# S4 method for 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

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)
#> DataFrame with 2 rows and 7 columns #> id cc1 cc2 cc3 #> <character> <numeric> <numeric> <numeric> #> 1 hsa-let-7a-5p 0 0 0 0 : TGAGGTAGTAGGTTGTATAGTT 235825 171354 149541 #> 2 hsa-let-7a-5p 0 0 0 t : TGAGGTAGTAGGTTGTATAGT 50920 52403 35525 #> ct2 ct3 ct4 #> <numeric> <numeric> <numeric> #> 1 163569 114028 123454 #> 2 35795 24993 34512