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)
| 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. |
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
Lorena Pantano
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 14 columns #> cc1 cc2 cc3 cc4 cc5 #> <numeric> <numeric> <numeric> <numeric> <numeric> #> hsa-let-7a-5p 235825 171354 149541 180654 168884 #> hsa-let-7a-5p;iso_3p:t 50920 52403 35525 53213 51499 #> cc6 cc7 ct1 ct2 ct3 #> <numeric> <numeric> <numeric> <numeric> <numeric> #> hsa-let-7a-5p 107430 153061 143030 163569 114028 #> hsa-let-7a-5p;iso_3p:t 30659 45492 42878 35795 24993 #> ct4 ct5 ct6 ct7 #> <numeric> <numeric> <numeric> <numeric> #> hsa-let-7a-5p 123454 133092 158909 140272 #> hsa-let-7a-5p;iso_3p:t 34512 36973 47873 39585