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.
#> pc2 pt2 pt7 pc1 pt6 pc3 pt3 pt5 #> hsa-let-7a-2-3p.iso 6 3 0 9 2 4 4 0 #> hsa-let-7a-2-3p.ref 5 4 10 4 2 9 5 3 #> hsa-let-7a-3p.iso 782 634 1002 1140 536 857 1169 380 #> hsa-let-7a-3p.ref 146 111 157 153 77 116 192 53 #> hsa-let-7a-5p.iso 96391 84487 126832 124343 76467 96519 136940 41708 #> hsa-let-7a-5p.ref 259187 239647 391118 382703 222561 279317 363483 110483 #> pt4 pc5 pc4 pc7 pc6 pt1 #> hsa-let-7a-2-3p.iso 0 7 10 4 5 0 #> hsa-let-7a-2-3p.ref 0 7 10 2 5 2 #> hsa-let-7a-3p.iso 888 1313 903 1050 516 444 #> hsa-let-7a-3p.ref 90 301 147 169 121 98 #> hsa-let-7a-5p.iso 98125 130896 136026 93118 58277 39226 #> hsa-let-7a-5p.ref 321629 337896 353169 247664 157358 111195# taking into account isomiRs and reference sequence. ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6) head(counts(ids))#> pc2 pt2 pt7 pc1 pt6 pc3 pt3 pt5 #> hsa-let-7a-3p.iso 782 634 1002 1140 536 857 1169 380 #> hsa-let-7a-3p.ref 146 111 157 153 77 116 192 53 #> hsa-let-7a-5p.iso 96391 84487 126832 124343 76467 96519 136940 41708 #> hsa-let-7a-5p.ref 259187 239647 391118 382703 222561 279317 363483 110483 #> hsa-let-7b-3p.iso 1966 1404 1589 1639 1051 1264 1992 566 #> hsa-let-7b-5p.iso 41690 31802 41571 50956 23576 35542 48289 13555 #> pt4 pc5 pc4 pc7 pc6 pt1 #> hsa-let-7a-3p.iso 888 1313 903 1050 516 444 #> hsa-let-7a-3p.ref 90 301 147 169 121 98 #> hsa-let-7a-5p.iso 98125 130896 136026 93118 58277 39226 #> hsa-let-7a-5p.ref 321629 337896 353169 247664 157358 111195 #> hsa-let-7b-3p.iso 1144 2852 1984 1722 875 749 #> hsa-let-7b-5p.iso 32629 46634 45151 32215 19793 14587