compMatrix {epihet} | R Documentation |
A matrix is created for pca/hclust/tsne which contains read number, average methylation levels, pdr, epipolymorphism, and Shannon entropy values across multiple samples at the same loci using read number in a GenomicRanges object
compMatrix(epi.gr, outprefix = NULL, readNumber = 60, p = 1, cores = 5, sve = FALSE)
epi.gr |
An input file containing the read number, locus, pdr, epipolymorphism, and Shannon entropy values stored in a list of GenomicRanges objects |
outprefix |
The prefix name of the outputted matrix file. 'sve' must be set to TRUE (default: NULL) |
readNumber |
The lowest number of reads required for each loci (default: 60) |
p |
Percentage (as decimal) of matching samples required to determine a match at a given locus, e.g. a value of 0.75 requires 75% of the samples to have an epiallele at a common loci in order to add the loci to the matrix (default: 1) |
cores |
The number of cores to be used for parallel execution (default: 5) |
sve |
A boolean to save the comparison matrix (default: FALSE) |
A large matrix containing values (pdr, etc.) at the same loci
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)) N1.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(112,112,112,68,76),values.meth1=c(82,60,91,71,90), values.shannon=c(0.15,0.26,0.34,0.24,0.15), values.pdr=c(0.32,0.57,0.37,0.37,0.13), values.epipoly=c(0.57,0.42,0.28,0.38,0.23)) N2.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(385,78,70,96,96),values.meth1=c(96,81,87,87,93), values.pdr=c(0.15,0.52,0.48,0.25,0.25), values.epipoly=c(0.26,0.58,0.58,0.37,0.37), values.shannon=c(0.12,0.25,0.54,0.23,0.25)) GR.List<-list(p1=p1.GR,p2=p2.GR,N1=N1.GR,N2=N2.GR) comp.Matrix <- compMatrix(epi.gr = GR.List, outprefix = NULL, readNumber = 60, p = 1, cores = 1, sve = FALSE)