Normalize count matrix

Description

This function normalizes raw count matrix using rlog function from DESeq2-package.

Usage

isoNorm(ids, formula = ~condition)

Arguments

Value

IsomirDataSeq object with the normalized count matrix in a slot. The normalized matrix can be access with counts(ids, norm=TRUE).

Examples

data(mirData)
ids <- isoCounts(mirData, minc=10, mins=6)
ids <- isoNorm(mirData, formula=~condition)
head(counts(ids, norm=TRUE))

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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> 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/isoNorm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: isoNorm
> ### Title: Normalize count matrix
> ### Aliases: isoNorm
> 
> ### ** Examples
> 
> data(mirData)
> ids <- isoCounts(mirData, minc=10, mins=6)
> ids <- isoNorm(mirData, formula=~condition)
converting counts to integer mode
> head(counts(ids, norm=TRUE))
                     nb1        nb2        nb3         o1         o2         o3
hsa-let-7a-3p  5.4229271  5.3715090  4.8964338  5.2599832  5.0589000  5.5277466
hsa-let-7a-5p 19.4536090 18.5069864 18.8082117 18.8097258 18.6140925 18.9119333
hsa-let-7b-3p  4.5456138  4.5587187  4.3635611  4.4185961  4.7718968  4.6430228
hsa-let-7b-5p 17.5339421 16.9009713 17.0378757 16.9465325 16.9315254 16.9935085
hsa-let-7c-3p -0.5054075 -0.5404369 -0.3158298 -0.5375628 -0.5329659 -0.2854954
hsa-let-7c-5p 19.5273039 18.2696821 18.5716813 18.4622236 18.3602766 18.4624296
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>