Commit 1f7ab37b authored by HYsxe's avatar HYsxe
Browse files

Remove BuenRTools dependency

parent 61b52eba

code/filterFrags.R

+1 −2
Original line number Original line Diff line number Diff line
@@ -30,4 +30,3 @@ fragsFilt <- frags %>% filter(V4 %in% colnames(scATACFilt)) 
fragsGz <- gzfile("all.frags.filt.tsv.gz", "w")

fragsGz <- gzfile("all.frags.filt.tsv.gz", "w")

write.table(fragsFilt, fragsGz, quote = F, sep = "\t", col.names = F, row.names = F)

write.table(fragsFilt, fragsGz, quote = F, sep = "\t", col.names = F, row.names = F)

close(fragsGz)
 
close(fragsGz)

code/filterPeaks.R

+1 −0
Original line number Original line Diff line number Diff line
@@ -37,4 +37,5 @@ summitsToCleanPeaks(summitFiles = paste0("peakCalling/", summitFile), 
                    resizeTo = 1000 # Re-size peaks after filtering?

                    resizeTo = 1000 # Re-size peaks after filtering?

)

)





# Rename file

system("mv peakCalling/filtered.fixedwidthpeaks_800bp_1000reSized.bed peaks.bed")
 
system("mv peakCalling/filtered.fixedwidthpeaks_800bp_1000reSized.bed peaks.bed")
 
 No newline at end of file

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