gatherEXPANDSoutput<-function(outDirEXPANDS,regex=""){
f=grep(regex,list.files(outDirEXPANDS,pattern="*.sps$",full.names = T),value=T)
expdata=list()
for(x in f){
sps=read.table(x,sep="\t",header = T,check.names = F,stringsAsFactors = F);
if(any(colnames(sps)=="LOCUS")){
rownames(sps)=sps$LOCUS
sps=sps[,setdiff(colnames(sps),"LOCUS")]
}
spstats=read.table(gsub(".sps$",".spstats",x),sep="\t",header = T,check.names = F,stringsAsFactors = F);
# ##TODO --> remove this column update: --> fixed to be correct for next expands version
# tmp=count(sps[,"SP"]); i=.intersect_MatlabV(round(tmp$x,3),round(spstats$`Mean Weighted`,3));
# spstats[i$ib,"nMutations"]=tmp$freq[i$ia]
# ##
if(file.exists(gsub(".sps$",".tree",x))){
tree=try(phylobase::readNewick(gsub(".sps$",".tree",x)))
treeApe=read.tree(gsub(".sps$",".tree",x))
}else{
tree=NULL; treeApe=NULL;
}
spscbs=try(read.table(gsub(".sps$",".sps.cbs",x),sep="\t",header = T,check.names = F,stringsAsFactors = F));
if(class(spscbs)!= "try-error"){
spscbs$seglength=1+spscbs$endpos-spscbs$startpos
if(any(colnames(spscbs)=="LOCUS")){
rownames(spscbs)=spscbs$LOCUS
spscbs=spscbs[,setdiff(colnames(spscbs),"LOCUS")]
}
}
sName=strsplit(fileparts(x)$name,".sps")[[1]][1]
expdata[[sName]]=list(snv=sps,cbs=as.matrix(spscbs),spstats=as.matrix(spstats),tree=tree, treeApe=treeApe)
}
return(expdata)
}
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