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