library (Rsamtools)
library (GenomicFeatures)
library (GenomicAlignments)
gtfFile = "Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
txdb = makeTxDbFromGFF (gtfFile, format= "gtf" )
genes = exonsBy (txdb, by= "gene" )
dirActualData = paste (getwd (),"/" ,sep= "" )
sampleTableSingle = read.table ("BamFiles.txt" )
fls = paste (dirActualData,sampleTableSingle[,1 ],sep= "" )
bamLst = BamFileList (fls, index= character (),yieldSize= 100000 ,obeyQname= TRUE )
PRJNA297798 = summarizeOverlaps (features = genes,read= bamLst,
mode= "Union" ,
singleEnd= TRUE ,
ignore.strand= TRUE ,
fragments= FALSE )
metadatos = read.csv ("PRJNA297798coldata.csv" ,header= TRUE ,sep= "," )
metadatos[,"strain" ] = factor (metadatos[,"strain" ],levels= 1 : 4 ,
labels= c ("daf-2(e1370);daf-16(mu86);Punc-119::gfp" ,
"daf-2(e1370);Punc-119::gfp" ,
"pmec-4::gfp" ,"Punc-119::gfp" ))
metadatos[,"tissue" ] = factor (metadatos[,"tissue" ],levels= 1 : 2 ,labels= c ("Neurons" ,"Whole worm" ))
metadatos[,"treatment" ] = factor (metadatos[,"treatment" ],levels= 1 : 6 ,
labels= c ("daf-2(e1370); daf-16(mu86); Punc-119::gfp--sorted neurons" ,
"daf-2(e1370) neurons" ,"N2; Pmec-4::GFP--sorted mechanosensory neurons" ,
"daf-2(e1370); Punc-119::gfp--sorted neurons" ,"N2; Punc-119::gfp--sorted neurons" ,
"N2; Punc-119::gfp--unsorted/whole worm" ))
colData (PRJNA297798) = DataFrame (metadatos)
colnames (PRJNA297798) = colData (PRJNA297798)[,"run" ]
save (PRJNA297798,file= "PRJNA297798.rda" )