comparison csaw.R @ 5:aa29b20bbb45 draft

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4:609b5a2ae0e8

# Final table with all windows and read counts ----
table <- data.frame(df, assay(windows), stringsAsFactors = F, check.names = F)
colnames(table)[4:ncol(table)] <- file_names


# Remove spaces in the table ----
setDT(table)
for (j in names(table)) set(table, j = j, value = table[[trimws(j)]]) 
table_sp <- data.frame(table)

# Save final table ----
fwrite(x = table_sp, file = output, quote = F, row.names = F, sep = "\t")

# # Save individual files ----
# Sys.time()
# r <- paste(table_sp[,1], table_sp[,2], table_sp[,3], sep = "-")
# Sys.time()

5:aa29b20bbb45

# Final table with all windows and read counts ----
table <- data.frame(df, assay(windows), stringsAsFactors = F, check.names = F)
colnames(table)[4:ncol(table)] <- file_names

# Remove spaces in the table ----
setDT(table)
for (j in names(table)) set(table, j = j, value = table[[trimws(j)]]) 

# Save final table ----
# fwrite(x = table_sp, file = output, quote = F, row.names = F, sep = "\t")
dt <- table[,regions:=paste0(seqnames,"-", start, "-", end)]
table_sp <- data.frame(dt)

for(i in 4:(ncol(table_sp)-1)){
  tmp <- table_sp[,c(ncol(table_sp), i)]
  fwrite(x = tmp, file = output, quote = F, row.names = F, sep = "\t")
}

# # Save individual files ----
# Sys.time()
# r <- paste(table_sp[,1], table_sp[,2], table_sp[,3], sep = "-")
# Sys.time()