#' bamMatching
#'
#' @param bam.datapath
#' @param param
#' @param h5name
#' @param h5PathOut
#'
#' @return
#' @keywords internal
#'
#' @examples
bamMatching <- function (bam.datapath, param, h5name='h5file', h5PathOut=''){
h5path<-h5PathOut
bamPathNoPrefix <- gsub('.bam', '', bam.datapath)
#prefixNam<-paste0(bamPathNoPrefix, '.h5')
prefixNam<-paste0(h5PathOut, h5name, '.h5')
hs.param<-param
diagnostics <- diffHic::preparePairs(bam.datapath, hs.param, file=prefixNam, dedup=TRUE, minq=10)
##===getPairData inseriscilo in una funzione per il QC
diags <- diffHic::getPairData(prefixNam, hs.param)
##show results
var_showw<-capture.output(as.data.frame(show (diagnostics)))
print (var_showw)
varshoww2<- strsplit(var_showw[2], " ")
varshoww3<- strsplit(var_showw[3], " ")
varshoww2<- as.vector (varshoww2[[1]])
varshoww2<- varshoww2[varshoww2 != ""]
varshoww3<- as.vector (varshoww3[[1]])
varshoww3<- varshoww3[varshoww3 != ""]
varmatrixpairs<- matrix(nrow=2,ncol=4)
#print (varshoww2)
#print (varshoww3)
varmatrixpairs[1,]<- varshoww2
varmatrixpairs[2,]<- varshoww3
print ('varmatrixpairs')
print (varmatrixpairs)
#print (varmatrixpairs)
varshoww6<- strsplit(var_showw[6], " ")
varshoww7<- strsplit(var_showw[7], " ")
varshoww6<- as.vector (varshoww6[[1]])
varshoww6<- varshoww6[varshoww6 != ""]
varshoww7<- as.vector (varshoww7[[1]])
varshoww7<- varshoww7[varshoww7 != ""]
varmatrixpairs2<- matrix(nrow=2,ncol=2)
varmatrixpairs2[1,]<- varshoww6
varmatrixpairs2[2,]<- varshoww7
print('varmatrixpairs2')
print(varmatrixpairs2)
#varshoww9<- strsplit(var_showw[9], " ")
varshoww9<- var_showw[9]
varshoww10<-var_showw[10]
#varshoww10<- strsplit(var_showw[10], " ")
#varshoww9<- as.vector (varshoww6[[1]])
#varshoww9<- varshoww6[varshoww6 != ""]
#varshoww10<- as.vector (varshoww10[[1]])
#varshoww10<- varshoww7[varshoww10 != ""]
varmatrixpairs3<- matrix(nrow=2,ncol=1)
varmatrixpairs3[1,]<- varshoww9
varmatrixpairs3[2,]<- varshoww10
print('varmatrixpairs3')
print(varmatrixpairs3)
#print (varshoww6)
#print (varshoww7)
#print ('varmatrixpairs fatta')
#print (varmatrixpairs)
#print (varmatrixpairs2)
varshoww13<- strsplit(var_showw[13], " ")
varshoww14<- strsplit(var_showw[14], " ")
varshoww13<- as.vector (varshoww13[[1]])
varshoww13<- varshoww13[varshoww13 != ""]
varshoww14<- as.vector (varshoww14[[1]])
varshoww14<- varshoww14[varshoww14 != ""]
print (varshoww13)
print (varshoww14)
varmatrixpairs4<- matrix(nrow=2,ncol=4)
varmatrixpairs4[1,]<- varshoww13
varmatrixpairs4[2,]<- varshoww14
print('varmatrixpairs4')
print (varmatrixpairs4)
print ('varmatrixpairs fatta')
#print (varmatrixpairs3)
#print (varmatrixpairs2)
#write.table (varmatrixpairs,file='varma', sep='\t',row.names=FALSE, col.names= FALSE )
#write.table (varmatrixpairs2,file='varma2', sep='\t',row.names=FALSE, col.names= FALSE )
#write.table (varmatrixpairs3,file='varma3', sep='\t',row.names=FALSE, col.names= FALSE )
varmaSum<-c(varmatrixpairs,varmatrixpairs2,varmatrixpairs3,varmatrixpairs4)
write.table (varmaSum,
file=paste0(h5PathOut, h5name, '_bamMatching_report'), sep='\t',row.names=FALSE, col.names= FALSE, quote=FALSE )
#varmatrixList<- list (var_showw,varmatrixpairs,varmatrixpairs2,varmatrixpairs3)
return (diagnostics)
}
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