countNMers: Count N Mers Find the weighted value of each nmer

In alexjgriffith/kmerhmm:

Description

Count N Mers Find the weighted value of each nmer

Usage

countNMers(fastaFile, weights, n = 6)

Arguments

fastaFile	The fasta file to be analyzed, each region must be represented in a single line
weights	a vector of weight the same length as the number of members in the fasta file
n	the number of ks

Examples

library(mulcal)
library(kmerhmm)
fastaFile<-"~/Dropbox/UTX-Alex/jan/combined.fasta"
heightFile<-"~/Dropbox/UTX-Alex/jan/combined_heights.bed"
temp<-read.table(heightFile)
data<-as.matrix(temp[,4:dim(temp)[2]])
dataLocs<-list(list("eryt", 1, "top"),
              list("tall", 1,"bottom"),
              list("ecfc",3,"top"),
              list("other",c(3,5),c("top","top")),
              list("meka",c(3,7),c("top","top")),
              list("hspc",c(3,7),c("top","bottom")),
              list("diff", 7, "top"))
normData<-qn(data)
prc<-prcomp(t(normData))$rotation
projection<-t(normData)%*%prc
weights<-prc[,1]
countNMers(fastaFile,weights,4)

alexjgriffith/kmerhmm documentation built on May 10, 2019, 8:53 a.m.