summarize: Summarize Data

Description Usage Arguments Value Examples

View source: R/summarize.R

Description

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

Usage

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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

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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.