This function collapses isomiRs into different groups. It is a similar concept than how to work with gene isoforms. With this function, different changes can be put together into a single miRNA variant. For instance all sequences with variants at 3' end can be considered as different elements in the table or analysis having the following naming hsa-miR-124a-5p.iso.t3:AAA.

isoCounts(ids, ref = FALSE, iso5 = FALSE, iso3 = FALSE, add = FALSE,
  subs = FALSE, seed = FALSE, minc = 1, mins = 1)

Arguments

ids

Object of class IsomirDataSeq.

ref

Differentiate reference miRNA from rest.

iso5

Differentiate trimming at 5 miRNA from rest.

iso3

Differentiate trimming at 3 miRNA from rest.

add

Differentiate additions miRNA from rest.

subs

Differentiate nt substitution miRNA from rest.

seed

Differentiate changes in 2-7 nts from rest.

minc

Int minimum number of isomiR sequences to be included.

mins

Int minimum number of samples with number of sequences bigger than minc counts.

Value

IsomirDataSeq object with new count table. The count matrix can be access with counts(ids).

Details

You can merge all isomiRs into miRNAs by calling the function only with the first parameter isoCounts(ids). You can get a table with isomiRs altogether and the reference miRBase sequences by calling the function with ref=TRUE. You can get a table with 5' trimming isomiRS, miRBase reference and the rest by calling with isoCounts(ids, ref=TRUE, iso5=TRUE). If you set up all parameters to TRUE, you will get a table for each different sequence mapping to a miRNA (i.e. all isomiRs).

Examples for the naming used for the isomiRs are at http://seqcluster.readthedocs.org/mirna_annotation.html#mirna-annotation.

Examples

data(mirData) ids <- isoCounts(mirData, ref=TRUE) head(counts(ids))
#> cc1 cc2 cc3 ct2 ct3 ct4 #> hsa-let-7a-2-3p.iso 2 7 2 0 2 6 #> hsa-let-7a-2-3p.ref 3 6 2 4 0 6 #> hsa-let-7a-3p.iso 653 593 543 448 312 553 #> hsa-let-7a-3p.ref 114 114 87 48 31 82 #> hsa-let-7a-5p.iso 81905 73478 54347 58497 40218 52069 #> hsa-let-7a-5p.ref 235825 171354 149541 163569 114028 123454
# taking into account isomiRs and reference sequence. ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6) head(counts(ids))
#> cc1 cc2 cc3 ct2 ct3 ct4 #> hsa-let-7a-3p.iso 653 593 543 448 312 553 #> hsa-let-7a-3p.ref 114 114 87 48 31 82 #> hsa-let-7a-5p.iso 81905 73478 54347 58497 40218 52069 #> hsa-let-7a-5p.ref 235825 171354 149541 163569 114028 123454 #> hsa-let-7b-3p.iso 1033 1729 668 808 483 1058 #> hsa-let-7b-5p.iso 31209 36938 18988 22156 14187 20585