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example: GenomicFiles MAP on GRangesList
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library(GenomicFiles) | |
register(SerialParam()) | |
# use 4 BigWigs from | |
# ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/ | |
files <- list.files("~/data/bigwig/",full=TRUE) | |
ranges0 <- GRanges("chr1",IRanges(11:20 * 1e6, width=1e5)) | |
f <- factor(rep(1:2, each=length(ranges0)/2)) | |
ranges <- split(ranges0, f) | |
MAP <- function(range, file) { | |
rle <- import(file, which = range, as = "Rle", format = "bw")[range] | |
mean(rle) | |
} | |
REDUCE <- function(mapped) { | |
Reduce(cbind, mapped) | |
} | |
(res <- reduceByRange(ranges, files, MAP, REDUCE)) | |
(resOut <- do.call(rbind, res)) | |
sessionInfo() |
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> register(SerialParam()) | |
> # use 4 BigWigs from | |
> # ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/ | |
> files <- list.files("~/data/bigwig/",full=TRUE) | |
> ranges0 <- GRanges("chr1",IRanges(11:20 * 1e6, width=1e5)) | |
> f <- factor(rep(1:2, each=length(ranges0)/2)) | |
> ranges <- split(ranges0, f) | |
> MAP <- function(range, file) { | |
+ rle <- import(file, which = range, as = "Rle", format = "bw")[range] | |
+ mean(rle) | |
+ } | |
> REDUCE <- function(mapped) { | |
+ Reduce(cbind, mapped) | |
+ } | |
> (res <- reduceByRange(ranges, files, MAP, REDUCE)) | |
$`1` | |
init | |
chr1 0.08394 0.08899 4.58022 3.49198 | |
chr1 0.04923 0.04763 10.90287 8.61417 | |
chr1 0.03631 0.04303 0.00780 0.00727 | |
chr1 0.03408 0.04532 2.16463 1.69084 | |
chr1 0.01378 0.00825 0.01869 0.00581 | |
$`2` | |
init | |
chr1 0.13007 0.07382 3.83418 3.69978 | |
chr1 0.91577 0.59110 50.07868 71.86047 | |
chr1 0.01693 0.04954 0.18872 0.17385 | |
chr1 0.00671 0.00805 0.20328 0.17623 | |
chr1 1.12673 0.94558 0.05567 0.04120 | |
> (resOut <- do.call(rbind, res)) | |
init | |
chr1 0.08394 0.08899 4.58022 3.49198 | |
chr1 0.04923 0.04763 10.90287 8.61417 | |
chr1 0.03631 0.04303 0.00780 0.00727 | |
chr1 0.03408 0.04532 2.16463 1.69084 | |
chr1 0.01378 0.00825 0.01869 0.00581 | |
chr1 0.13007 0.07382 3.83418 3.69978 | |
chr1 0.91577 0.59110 50.07868 71.86047 | |
chr1 0.01693 0.04954 0.18872 0.17385 | |
chr1 0.00671 0.00805 0.20328 0.17623 | |
chr1 1.12673 0.94558 0.05567 0.04120 | |
> sessionInfo() | |
R Under development (unstable) (2014-09-25 r66681) | |
Platform: x86_64-apple-darwin12.5.0 (64-bit) | |
locale: | |
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | |
attached base packages: | |
[1] stats4 parallel stats graphics grDevices datasets utils | |
[8] methods base | |
other attached packages: | |
[1] GenomicFiles_1.1.19 BiocParallel_0.99.22 futile.logger_1.3.7 | |
[4] rtracklayer_1.25.16 Rsamtools_1.17.34 Biostrings_2.33.14 | |
[7] XVector_0.5.8 GenomicRanges_1.17.42 GenomeInfoDb_1.1.23 | |
[10] IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5 | |
[13] RUnit_0.4.27 devtools_1.6 slidify_0.4.5 | |
[16] knitr_1.6 BiocInstaller_1.15.5 | |
loaded via a namespace (and not attached): | |
[1] base64enc_0.1-2 BatchJobs_1.4 BBmisc_1.7 | |
[4] bitops_1.0-6 brew_1.0-6 checkmate_1.4 | |
[7] codetools_0.2-9 DBI_0.3.1 digest_0.6.4 | |
[10] evaluate_0.5.5 fail_1.2 foreach_1.4.2 | |
[13] formatR_1.0 futile.options_1.0.0 GenomicAlignments_1.1.30 | |
[16] iterators_1.0.7 lambda.r_1.1.6 markdown_0.7.4 | |
[19] RCurl_1.95-4.3 RSQLite_0.11.4 sendmailR_1.2-1 | |
[22] stringr_0.6.2 tools_3.2.0 whisker_0.3-2 | |
[25] XML_3.98-1.1 yaml_2.1.13 zlibbioc_1.11.1 | |
> |
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