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Last data update: 2014.03.03

R: Alignment statistics

alignStats

R Documentation

Alignment statistics

Description

Generate data frame containing important read alignment statistics such as the total number of reads in the FASTQ files, the number of total alignments, as well as the number of primary alignments in the corresponding BAM files.

Usage

alignStats(args)

Arguments

args

Object of class SYSargs.

Value

data.frame with alignment statistics.

Author(s)

Thomas Girke

Examples

## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
args
names(args); modules(args); cores(args); outpaths(args); sysargs(args)

## Not run: 
## Execute SYSargs on single machine
runCommandline(args=args)

## Execute SYSargs on multiple machines  
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR")
## Alignment stats
read_statsDF <- alignStats(args) 
read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## End(Not run)

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 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
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/systemPipeR/alignStats.Rd_%03d_medium.png", width=480, height=480)
> ### Name: alignStats
> ### Title: Alignment statistics
> ### Aliases: alignStats
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Construct SYSargs object from param and targets files 
> param <- system.file("extdata", "tophat.param", package="systemPipeR")
> targets <- system.file("extdata", "targets.txt", package="systemPipeR")
> args <- systemArgs(sysma=param, mytargets=targets)
There were 18 warnings (use warnings() to see them)
> args
An instance of 'SYSargs' for running 'tophat' on 18 samples 
> names(args); modules(args); cores(args); outpaths(args); sysargs(args)
 [1] "targetsin"     "targetsout"    "targetsheader" "modules"      
 [5] "software"      "cores"         "other"         "reference"    
 [9] "results"       "infile1"       "infile2"       "outfile1"     
[13] "sysargs"       "outpaths"     
[1] "bowtie2/2.2.5" "tophat/2.0.14"
[1] 4
                                                                                    M1A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat/accepted_hits.bam" 
                                                                                    M1B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat/accepted_hits.bam" 
                                                                                    A1A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat/accepted_hits.bam" 
                                                                                    A1B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat/accepted_hits.bam" 
                                                                                    V1A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat/accepted_hits.bam" 
                                                                                    V1B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat/accepted_hits.bam" 
                                                                                    M6A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat/accepted_hits.bam" 
                                                                                    M6B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat/accepted_hits.bam" 
                                                                                    A6A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat/accepted_hits.bam" 
                                                                                    A6B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat/accepted_hits.bam" 
                                                                                    V6A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat/accepted_hits.bam" 
                                                                                    V6B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat/accepted_hits.bam" 
                                                                                   M12A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat/accepted_hits.bam" 
                                                                                   M12B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat/accepted_hits.bam" 
                                                                                   A12A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat/accepted_hits.bam" 
                                                                                   A12B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat/accepted_hits.bam" 
                                                                                   V12A 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat/accepted_hits.bam" 
                                                                                   V12B 
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat/accepted_hits.bam" 
                                                                                                                                                                                                       M1A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446027_1.fastq " 
                                                                                                                                                                                                       M1B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446028_1.fastq " 
                                                                                                                                                                                                       A1A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446029_1.fastq " 
                                                                                                                                                                                                       A1B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446030_1.fastq " 
                                                                                                                                                                                                       V1A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446031_1.fastq " 
                                                                                                                                                                                                       V1B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446032_1.fastq " 
                                                                                                                                                                                                       M6A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446033_1.fastq " 
                                                                                                                                                                                                       M6B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446034_1.fastq " 
                                                                                                                                                                                                       A6A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446035_1.fastq " 
                                                                                                                                                                                                       A6B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446036_1.fastq " 
                                                                                                                                                                                                       V6A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446037_1.fastq " 
                                                                                                                                                                                                       V6B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446038_1.fastq " 
                                                                                                                                                                                                      M12A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446039_1.fastq " 
                                                                                                                                                                                                      M12B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446040_1.fastq " 
                                                                                                                                                                                                      A12A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446041_1.fastq " 
                                                                                                                                                                                                      A12B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446042_1.fastq " 
                                                                                                                                                                                                      V12A 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446043_1.fastq " 
                                                                                                                                                                                                      V12B 
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446044_1.fastq " 
> 
> ## Not run: 
> ##D ## Execute SYSargs on single machine
> ##D runCommandline(args=args)
> ##D 
> ##D ## Execute SYSargs on multiple machines  
> ##D qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00")
> ##D qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR")
> ##D ## Alignment stats
> ##D read_statsDF <- alignStats(args) 
> ##D read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
> ##D write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>