create_count_matrix.R

library(isomiRs)

#https://rdrr.io/github/lpantano/isomiRs/man/IsomirDataSeqFromFiles.html

path <- "/data/data_fastq/reads_colapsed/aligner_output_mirna"
fn_list <- list.files(path, pattern="mirna", full.names = TRUE)
de <- data.frame(fn_list)
ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)
count_matrix<-counts(ids)
colnames(count_matrix)<-list.files(path, pattern="mirna")
write.csv(count_matrix, file="count_matrix.csv")


#head(counts(ids))
#IsomirDataSeqFromRawData(metadata(ids)[["rawData"]], de)
#http://lpantano.github.io/isomiRs/reference/isoCounts.html
#data(mirData)
#ids <- isoCounts(mirData, ref=TRUE)
#head(counts(ids))