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,
  subs = FALSE, seed = FALSE, minc = 1, mins = 1)

Arguments

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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(isomiRs)
Loading required package: DiscriMiner
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/isomiRs/isoCounts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isoCounts
> ### Title: Create count matrix with different summarizing options
> ### Aliases: isoCounts
> 
> ### ** Examples
> 
> data(mirData)
> ids <- isoCounts(mirData, ref=TRUE)
> head(counts(ids))
                     nb1    nb2    nb3     o1     o2     o3
hsa-let-7a-3p.iso     16     45     14     28     19     50
hsa-let-7a-3p.ref      8     25      9     19      7     15
hsa-let-7a-5p.iso  98799 117213  91493 117138  80728 125977
hsa-let-7a-5p.ref 328816 427450 335726 439522 245117 499625
hsa-let-7b-3p.iso     12     38     17     24     27     33
hsa-let-7b-5p.iso  39957  61305  43601  42921  36954  42320
> # taking into account isomiRs and reference sequence.
> ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6)
> head(counts(ids))
                     nb1    nb2    nb3     o1     o2     o3
hsa-let-7a-3p.iso     16     45     14     28     19     50
hsa-let-7a-5p.iso  98799 117213  91493 117138  80728 125977
hsa-let-7a-5p.ref 328816 427450 335726 439522 245117 499625
hsa-let-7b-3p.iso     12     38     17     24     27     33
hsa-let-7b-5p.iso  39957  61305  43601  42921  36954  42320
hsa-let-7b-5p.ref  69810 127089  82385 107306  67639 117933
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>