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 4 rows and 15 columns #> id pc1 pc2 pc3 #> <character> <numeric> <numeric> <numeric> #> 1 hsa-let-7a-5p 0 0 0 0 : TGAGGTAGTAGGTTGTATAGTT 382703 259187 279317 #> 2 hsa-let-7a-5p 0 0 0 t : TGAGGTAGTAGGTTGTATAGT 76284 65140 62420 #> 3 hsa-let-7a-5p 0 0 0 T : TGAGGTAGTAGGTTGTATAGTTT 14582 9490 10487 #> 4 hsa-let-7a-5p 0 A 0 0 : TGAGGTAGTAGGTTGTATAGTTA 15438 7826 10425 #> pc4 pc5 pc6 pc7 pt1 pt2 pt3 #> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric> #> 1 353169 337896 157358 247664 111195 239647 363483 #> 2 91323 89100 39450 63273 25631 57218 90108 #> 3 13063 12455 5908 9233 4481 8640 14828 #> 4 12032 10865 5021 8075 3677 7523 13486 #> pt4 pt5 pt6 pt7 #> <numeric> <numeric> <numeric> <numeric> #> 1 321629 110483 222561 391118 #> 2 60010 27788 50366 79196 #> 3 12396 4467 8337 15646 #> 4 13765 3728 7498 15605