Question: Create a sample file /tab delimited file in QuasR
3.3 years ago by
Guest User • 12k
Guest User • 12k wrote:
I am somewhat new to R and am trying to load a file into QuasR. I downloaded the file e coli chip-seq data set SRR653521.sra from NCBIs SRA database (SRA accession number: SRX220452, GEO accession number: GSM1072327). I used ncbi sratoolkit to convert this to SRR653521.fastq. I am trying to load this into R using QuasR to do alignment, GO/pathway analysis, etc, but first need to get the fastq data into R for use with QuasR. I am using Windows 7, with current R, Bioconductor, and required packages. I followed the vignette found with browseVignettes(), and opened "An Introduction to QuasR". As in section 2.3, I loaded: library(QuasR) library(BSgenome) library(Rsamtools) library(rtracklayer) library(GenomicFeatures) library(Gviz) as well as library(ShortRead) for the reference genome I typed: available.genomes(); genomeName="BSgenome.Ecoli.NCBI.20080805" and for the sample file, I initially tried: sampleFile=readFastq("C:\\Users\\Chris\\Documents\\SRA\\SRX220452\\SRR 653521\\SRR653521.fastq") This did not work, so I tried to make a matrix for use in writing a tab delimited sample file, but was unsuccessful: > sampleMatrix=matrix(c("C:\\Users\\Chris\\Documents\\SRA\\SRX220452\\ SRR653521\\SRR653521.fastq"=FileName, Sample1=SampleName),nrow=2,ncol=2,byrow=TRUE) Error in matrix(c(`C:\\Users\\Chris\\Documents\\SRA\\SRX220452\\SRR653 521\\SRR653521.fastq` = FileName, : object 'FileName' not found > sampleMatrix=matrix(c("C:\\Users\\Chris\\Documents\\SRA\\SRX220452\\ SRR653521\\SRR653521.fastq", Sample1),nrow=2,ncol=2,byrow=TRUE, dimnames=c(flies,samples) + ) Error in matrix(c("C:\\Users\\Chris\\Documents\\SRA\\SRX220452\\SRR653 521\\SRR653521.fastq", : object 'Sample1' not found Can somebody please tell give me an example of code/syntax that will allow me to create a sample file? Also, I am not sure if my fastq file is for single end read, or paired end read. The examples listed in the vignette are only for files found in the "extdata" folder, and I don't know how to proceed. As soon as I get a sample file, I can probably figure out the rest. I hope this question isn't too basic, and thanks in advance for any help! -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  grid parallel stats graphics grDevices utils datasets methods base other attached packages:  BSgenome.Ecoli.NCBI.20080805_1.3.17 BiocInstaller_1.12.0 Gviz_1.6.0 GenomicFeatures_1.14.0  AnnotationDbi_1.24.0 Biobase_2.22.0 rtracklayer_1.22.0 BSgenome_1.30.0  ShortRead_1.20.0 Rsamtools_1.14.1 lattice_0.20-24 Biostrings_2.30.0  QuasR_1.2.0 Rbowtie_1.2.0 GenomicRanges_1.14.3 XVector_0.2.0  IRanges_1.20.3 BiocGenerics_0.8.0 loaded via a namespace (and not attached):  biomaRt_2.18.0 biovizBase_1.10.0 bitops_1.0-6 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 Hmisc_3.12-2  hwriter_1.3 labeling_0.2 latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 rpart_4.1-3  RSQLite_0.11.4 scales_0.2.3 stats4_3.0.2 stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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