Accessors for the count matrix of a IsomirDataSeq object.

Description

The counts slot holds the count data as a matrix of non-negative integer count values, one row for each isomiR, and one column for each sample. The normalized matrix can be obtained by using the parameter norm=TRUE.

Usage

counts.IsomirDataSeq(object, norm = FALSE)

## S4 method for signature 'IsomirDataSeq'
counts(object, norm = FALSE)

## S4 replacement method for signature 'IsomirDataSeq,matrix'
counts(object) <- value

Arguments

Value

matrix with raw or normalized count data.

Author(s)

Lorena Pantano

Examples

data(mirData)
head(counts(mirData))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/counts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts
> ### Title: Accessors for the count matrix of a IsomirDataSeq object.
> ### Aliases: counts counts,IsomirDataSeq-method counts.IsomirDataSeq
> ###   counts<-,IsomirDataSeq,matrix-method
> 
> ### ** Examples
> 
> data(mirData)
> head(counts(mirData))
                 nb1    nb2    nb3     o1     o2     o3
hsa-let-7a-3p     24     70     23     47     26     65
hsa-let-7a-5p 427615 544663 427219 556660 325845 625602
hsa-let-7b-3p     12     38     17     24     27     33
hsa-let-7b-5p 109767 188394 125986 150227 104593 160253
hsa-let-7c-3p      0      0      2      0      0      3
hsa-let-7c-5p 481931 462630 363116 425470 272375 434007
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>