IsomirDataSeqFromFiles loads miRNA annotation from seqbuster tool

Description

This function parses output of seqbuster tool to allow isomiRs/miRNAs analysis of samples in different groups such as characterization, differential expression and clustering. It creates an IsomirDataSeq object.

Usage

IsomirDataSeqFromFiles(files, design, header = FALSE, skip = 1,
  quiet = TRUE, ...)

Arguments

Details

This function parses the output of http://seqcluster.readthedocs.org/mirna_annotation.html for each sample to create a count matrix for isomiRs, miRNAs or isomiRs grouped in types (i.e all sequences with variations at 5' but ignoring any other type). It creates IsomirDataSeq object (see link to example usage of this class) to allow visualization, queries, differential expression analysis and clustering. To create the IsomirDataSeq, it parses the isomiRs files, and generates an initial matrix having all isomiRs detected among samples. As well, it creates a summary for each isomiR type (trimming, addition and substitution) to visualize general isomiRs distribution.

Value

IsomirDataSeq class object.

Examples

path <- system.file("extra", package="isomiRs")
fn_list <- list.files(path, full.names = TRUE)
de <- data.frame(row.names=c("f1" , "f2"), condition = c("newborn", "newborn"))
ids <- IsomirDataSeqFromFiles(fn_list, design=de)

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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> 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/IsomirDataSeqFromFiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IsomirDataSeqFromFiles
> ### Title: 'IsomirDataSeqFromFiles' loads miRNA annotation from seqbuster
> ###   tool
> ### Aliases: IsomirDataSeqFromFiles
> 
> ### ** Examples
> 
> path <- system.file("extra", package="isomiRs")
> fn_list <- list.files(path, full.names = TRUE)
> de <- data.frame(row.names=c("f1" , "f2"), condition = c("newborn", "newborn"))
> ids <- IsomirDataSeqFromFiles(fn_list, design=de)
> 
> head(counts(ids))
              f1 f2
hsa-let-7a-5p  0 19
hsa-let-7b-5p  1  6
hsa-let-7c-5p  5 64
hsa-let-7d-5p  0  1
hsa-let-7f-5p  8  8
hsa-let-7g-5p 74  4
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>