Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Class RqcResultSetDescriptionClass RqcResultSet Frequency distribution of cycle-specific base call Frequency distribution of cycle-specific quality File information Top over-represented sequencing reads Read frequency table Frequency distribution of per read mean quality Frequency distribution of read width UsageperCycleBasecall(x) ## S4 method for signature 'RqcResultSet' perCycleBasecall(x) ## S4 method for signature 'list' perCycleBasecall(x) perCycleQuality(x) ## S4 method for signature 'RqcResultSet' perCycleQuality(x) ## S4 method for signature 'list' perCycleQuality(x) perFileInformation(x) ## S4 method for signature 'RqcResultSet' perFileInformation(x) ## S4 method for signature 'list' perFileInformation(x) perFileTopReads(x) ## S4 method for signature 'RqcResultSet' perFileTopReads(x) ## S4 method for signature 'list' perFileTopReads(x) perReadFrequency(x) ## S4 method for signature 'RqcResultSet' perReadFrequency(x) ## S4 method for signature 'list' perReadFrequency(x) perReadQuality(x) ## S4 method for signature 'RqcResultSet' perReadQuality(x) ## S4 method for signature 'list' perReadQuality(x) perReadWidth(x) ## S4 method for signature 'RqcResultSet' perReadWidth(x) ## S4 method for signature 'list' perReadWidth(x) Arguments
Valuedata frame data frame data frame data frame data frame data frame data frame Examples
checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
files <- list.files(full.names=TRUE, path=folder)
rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
}, keep="rqcResultSet")
head(perCycleBasecall(rqcResultSet))
head(perCycleQuality(rqcResultSet))
head(perReadFrequency(rqcResultSet))
head(perReadQuality(rqcResultSet))
head(perReadWidth(rqcResultSet))
perFileInformation(rqcResultSet)
perFileTopReads(rqcResultSet)
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Rqc)
Loading required package: BiocParallel
Loading required package: ShortRead
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: Biostrings
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: IRanges
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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")'.
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rqc/RqcResultSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RqcResultSet-class
> ### Title: Class RqcResultSet
> ### Aliases: RqcResultSet-class perCycleBasecall
> ### perCycleBasecall,RqcResultSet-method perCycleBasecall,list-method
> ### perCycleQuality perCycleQuality,RqcResultSet-method
> ### perCycleQuality,list-method perFileInformation
> ### perFileInformation,RqcResultSet-method perFileInformation,list-method
> ### perFileTopReads perFileTopReads,RqcResultSet-method
> ### perFileTopReads,list-method perReadFrequency
> ### perReadFrequency,RqcResultSet-method perReadFrequency,list-method
> ### perReadQuality perReadQuality,RqcResultSet-method
> ### perReadQuality,list-method perReadWidth
> ### perReadWidth,RqcResultSet-method perReadWidth,list-method
>
> ### ** Examples
>
> checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
+ folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
+ files <- list.files(full.names=TRUE, path=folder)
+ rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
+ }, keep="rqcResultSet")
/home/ddbj/local/lib64/R/library/Rqc/extdata/Rqc.rda has been loaded.
> head(perCycleBasecall(rqcResultSet))
cycle base count filename
1 1 A 2248 ERR127302_1_subset.fastq.gz
2 1 C 10283 ERR127302_1_subset.fastq.gz
3 1 G 3105 ERR127302_1_subset.fastq.gz
4 1 T 4344 ERR127302_1_subset.fastq.gz
5 1 N 20 ERR127302_1_subset.fastq.gz
6 2 A 4965 ERR127302_1_subset.fastq.gz
> head(perCycleQuality(rqcResultSet))
cycle quality score count filename group
1 1 ! 0 0 ERR127302_1_subset.fastq.gz None
2 1 " 1 0 ERR127302_1_subset.fastq.gz None
3 1 # 2 5 ERR127302_1_subset.fastq.gz None
4 1 $ 3 0 ERR127302_1_subset.fastq.gz None
5 1 % 4 2 ERR127302_1_subset.fastq.gz None
6 1 & 5 9 ERR127302_1_subset.fastq.gz None
> head(perReadFrequency(rqcResultSet))
occurrence count filename
1 1 19291 ERR127302_1_subset.fastq.gz
2 2 247 ERR127302_1_subset.fastq.gz
3 3 34 ERR127302_1_subset.fastq.gz
4 4 18 ERR127302_1_subset.fastq.gz
5 5 3 ERR127302_1_subset.fastq.gz
6 6 2 ERR127302_1_subset.fastq.gz
> head(perReadQuality(rqcResultSet))
average count filename group
1 2.000000 5 ERR127302_1_subset.fastq.gz None
2 2.388889 2 ERR127302_1_subset.fastq.gz None
3 2.805556 1 ERR127302_1_subset.fastq.gz None
4 5.388889 1 ERR127302_1_subset.fastq.gz None
5 5.569444 1 ERR127302_1_subset.fastq.gz None
6 5.833333 1 ERR127302_1_subset.fastq.gz None
> head(perReadWidth(rqcResultSet))
width count filename
1 72 20000 ERR127302_1_subset.fastq.gz
2 72 20000 ERR127302_2_subset.fastq.gz
> perFileInformation(rqcResultSet)
filename pair format group reads total.reads
1 ERR127302_1_subset.fastq.gz 1 FASTQ None 20000 20000
2 ERR127302_2_subset.fastq.gz 1 FASTQ None 20000 20000
path
1 /home/welliton/R/x86_64-pc-linux-gnu-library/3.2/ShortRead/extdata/E-MTAB-1147
2 /home/welliton/R/x86_64-pc-linux-gnu-library/3.2/ShortRead/extdata/E-MTAB-1147
> perFileTopReads(rqcResultSet)
count filename
1 7 ERR127302_1_subset.fastq.gz
2 7 ERR127302_1_subset.fastq.gz
3 6 ERR127302_1_subset.fastq.gz
4 6 ERR127302_1_subset.fastq.gz
5 5 ERR127302_1_subset.fastq.gz
6 5 ERR127302_1_subset.fastq.gz
7 5 ERR127302_1_subset.fastq.gz
8 4 ERR127302_1_subset.fastq.gz
9 4 ERR127302_1_subset.fastq.gz
10 4 ERR127302_1_subset.fastq.gz
11 7 ERR127302_2_subset.fastq.gz
12 7 ERR127302_2_subset.fastq.gz
13 7 ERR127302_2_subset.fastq.gz
14 7 ERR127302_2_subset.fastq.gz
15 6 ERR127302_2_subset.fastq.gz
16 5 ERR127302_2_subset.fastq.gz
17 5 ERR127302_2_subset.fastq.gz
18 5 ERR127302_2_subset.fastq.gz
19 5 ERR127302_2_subset.fastq.gz
20 5 ERR127302_2_subset.fastq.gz
reads
1 GTTTGGTCTAGGGTGTAGCCTGAGAATAGGGGAAATCAGTGAATGAAGCCTCCTATGATGGCAAATACAGCT
2 CTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGC
3 CGATAACGTTGTAGATGTGGTCGTTACCTAGAAGGTTGCCTGGCTGGCCCAGCTCGGCTCGAATAAGGAGGC
4 CTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTA
5 CCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGCCT
6 CTGAGATGTTAGTATTAGTTAGTTTTGTTGTGAGTGTTAGGAAAAGGGCATACAGGACTAGGAAGCAGATAA
7 CACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCG
8 CAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGG
9 CAAGGAGTCGCAGGTCGCCTGGTTCTAGGAATAATGGGGGAAGTATGTAGGAGTTGAAGATTAGTCCGCCGT
10 TGCAGGTAGAGGCTTACTAGAAGTGTGAAAACGTAGGCTTGGATTAAGGCGACAGCGATTTCTAGGATAGTC
11 CGATAACGTTGTAGATGTGGTCGTTACCTAGAAGGTTGCCTGGCTGGCCCAGCTCGGCTCGAATAAGGAGGC
12 CGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGG
13 CGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGAC
14 CTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTA
15 TAGACATCGTACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTAT
16 CGGTAATGATGTCGGGGTTGAGGGATAGGAGGAGAATGGGGGATAGGTGTATGAACATGAGGGTGTTTTCTC
17 TGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTC
18 TGTGAGTGTAAATTAGTGCGATGAGTAGGGGAAGGGAGCCTACTAGGGTGTAGAATAGGAAGTATGTGCCTG
19 CAGGTAGAGGCTTACTAGAAGTGTGAAAACGTAGGCTTGGATTAAGGCGACAGCGATTTCTAGGATAGTCAG
20 CAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTT
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and