summarize: Summarize Data

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

Summarizes pdr, epipolymorphism, and shannon values over the annotation regions

Usage

summarize(gr1, gr2, value1, value2, cutoff1 = 10, cutoff2 = 60)

Arguments

gr1	A GenomicRanges object to be compared
gr2	A GenomicRanges object to be compared
value1	The value of gr1 to be compared
value2	The value of gr2 be compared
cutoff1	The first cutoff value for the number of reads (default:10)
cutoff2	The second cutoff value for the number of reads (default:60)

Value

A data frame containing a summary of the GenomicRanges object

Examples

p1.GR<-GRanges(seqnames = Rle(c("chr22"), c(5)),
ranges = IRanges(c(327,821,838,755,761), end = c(364,849,858,773,781)),
strand = Rle(strand(c("-", "+", "+", "+", "-"))),
values.loci = c("327:350:361:364","821:837:844:849",
"838:845:850:858","755:761:771:773","761:771:773:781"),
values.read1 = c(92,72,68,176,176),values.meth1=c(84,93,94,96,95),
values.shannon=c(0.4,0.5,0.5,0.2,0.5),values.pdr=c(0.6,0.25,0.23,0.15,0.17),
values.epipoly=c(0.48,0.42,0.38,0.27,0.3))

p2.GR<-GRanges(seqnames = Rle(c("chr22"), c(5)),
ranges = IRanges(c(327,821,838,755,761), end = c(364,849,858,773,781)),
strand = Rle(strand(c("-", "+", "+", "+", "-"))),
values.loci = c("327:350:361:364","821:837:844:849",
"838:845:850:858","755:761:771:773","761:771:773:781"),
values.read1 = c(107,102,102,76,76),values.meth1=c(88,66,69,71,94),
values.shannon=c(0.12,0.25,0.54,0.23,0.25),
values.pdr=c(0.38,1,0.97,1,0.13),
values.epipoly=c(0.57,0.42,0.28,0.18,0.23))

GR.List<-list(p1=p1.GR,p2=p2.GR)
summary <- summarize(gr1 = GR.List[[1]], gr2 = GR.List[[2]],
value1 = 'pdr', value2 = 'epipoly',
cutoff1 = 10, cutoff2 = 60)

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.