summarize {epihet}R Documentation

Summarize 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)

[Package epihet version 1.0.0 Index]