Katarzyna Wreczycka katwre

Bioinformatics Data Scientist

katwre / getData.R

Last active August 29, 2015 14:19

Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

	# RRBS from ENCODE
	rrbs.IMR90.path <- "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/wgEncodeHaibMethylRrbsImr90UwSitesRep1.bed.gz"
	rrbs.H1.path <- "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/wgEncodeHaibMethylRrbsH1hescHaibSitesRep1.bed.gz"

	# read the RRBS data to GRanges
	library(genomation)

	rrbs.IMR90<-readGeneric(rrbs.IMR90.path, chr = 1, start = 2, end = 3, strand = 6,
	meta.cols = list(score=11), keep.all.metadata = FALSE, zero.based = T, skip = 1)
	rrbs.H1<-readGeneric(rrbs.H1.path, chr = 1, start = 2, end = 3, strand = 6,

katwre / plot_comp.R

Created April 9, 2015 14:19

	plot(t1, type="l", col="red",
	xlab="", ylab="time [sec]",
	xaxt = "n", ylim=c(0, max(t1, t2)))
	lines(t2, type="l", col="blue")
	title(xlab = "number of rows of bigger dataset", line = 5)
	par(las=2)
	options(scipen=999) #disable scientific notation
	axis(1, at=seq(10,200, 10),
	labels=nmb.rows[seq(10, length(nmb.rows), 10)])
	legend("bottomright", c("findOverlaps","foverlaps"),

katwre / comp_foverlaps_findoverlaps.R

Last active August 29, 2015 14:18

Comparison the execution time of foverlaps and findOverlaps functions

	library(rbenchmark)
	library(GenomicRanges)
	library(data.table)

	# create sample dataset
	start <- seq(1L, 20e8L, 1000L)
	end <- start + 3000L
	chrom <- "chr1"
	DT.big <- data.table(chrom, start, end)

katwre / first_script.py

Last active August 29, 2015 14:18

First Gist

print "Hello world"