isoCounts {isomiRs} | R Documentation

## Create count matrix with different summarizing options

### Description

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`.

### Usage

    isoCounts(
      ids,
      ref = FALSE,
      iso5 = FALSE,
      iso3 = FALSE,
      add = FALSE,
      snv = FALSE,
      seed = FALSE,
      all = FALSE,
      minc = 1,
      mins = 1,
      merge_by = NULL
    )

### 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.
`snv` | Differentiate nt substitution miRNA from rest.
`seed` | Differentiate changes in 2-7 nts from rest.
`all` | Differentiate all isomiRs.
`minc` | Int minimum number of isomiR sequences to be included.
`mins` | Int minimum number of samples with number of sequences bigger than `minc` counts.
`merge_by` | Column in coldata to merge samples into a single column in counts. Useful to combine technical replicates.

### 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.

### Value

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

### Examples

    data(mirData)
    ids <- isoCounts(mirData, ref=TRUE)
    head(counts(ids))
    # taking into account isomiRs and reference sequence.
    ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6)
    head(counts(ids))

[Package isomiRs version 1.16.2 Index]