Mercurial > repos > dktanwar > test_csaw_1
comparison csaw.R @ 3:ce3ad612a104 draft
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| author | dktanwar |
|---|---|
| date | Mon, 18 Dec 2017 11:20:06 -0500 |
| parents | 66356a1014b1 |
| children | aa29b20bbb45 |
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| 2:ed929b85b051 | 3:ce3ad612a104 |
|---|---|
| 13 | 13 |
| 14 library("csaw") | 14 library("csaw") |
| 15 library("stringr") | 15 library("stringr") |
| 16 library("data.table") | 16 library("data.table") |
| 17 library("getopt") | 17 library("getopt") |
| 18 library("Rsamtools") | |
| 18 | 19 |
| 19 | 20 |
| 20 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) | 21 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) |
| 21 # Take in trailing command line arguments | 22 # Take in trailing command line arguments |
| 22 | 23 |
| 26 print(output) | 27 print(output) |
| 27 print(inputs) | 28 print(inputs) |
| 28 | 29 |
| 29 # Separate multiple input files into a list of individual files | 30 # Separate multiple input files into a list of individual files |
| 30 files <- unlist(strsplit(inputs, ',')) | 31 files <- unlist(strsplit(inputs, ',')) |
| 32 | |
| 33 # Index bamfiles | |
| 34 indexBam(files = files) | |
| 31 | 35 |
| 32 # Create windows and count reads in them ---- | 36 # Create windows and count reads in them ---- |
| 33 Sys.time() | 37 Sys.time() |
| 34 windows <- windowCounts(files, spacing=150, width=200, bin=F) | 38 windows <- windowCounts(files, spacing=150, width=200, bin=F) |
| 35 Sys.time() | 39 Sys.time() |