Modeling non-uniformity in short-read rates in RNA-Seq data

Documentation for package ‘mseq’ version 1.1

mseq-package	Modeling non-uniformity in short-read rates in RNA-Seq data
CVTrainIndexGene	CV index matrix
expData	expand the surrounding sequences
expData2nt	expand the surrounding sequences, including both the single nucleotide and dinucleotide composition
g1_part	a part of g1.csv
getDev	Poisson deviance
getNullCount	counts under null model
getOriLogPref	initialize for mart
getPredCount	predicted counts
getWeight	weight vector
glmPred	predict using iterative glm
glmPred2nt	predict using iterative glm with dinucleotide composition
iterGlm	iterative generalized linear regression
iterGlm2nt	iterative generalized linear regression using dinucleotide composition
iterGlmCV	cross-validation for iterative glm
iterGlmCV2nt	cross-validation for iterative glm using dinucleotide composition
martCV	cross-validation for MART
martPred	predict using MART
martTrain	train using MART
mseq	Modeling non-uniformity in short-read rates in RNA-Seq data
plotCoef	plot coefficients of Poisson linear model
plotCounts	plot counts
setOriOffset	initialize
updateOffset	update offsets