EBSeqTest: EBSeq core

In wiscstatman/EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

EBSeq core

Description

core function of EBSeq computation. Users are expected to use the wrappers, 2 conditions scenario, using EBTest, more than 2 condtiions, using EBMultiTest

Usage

EBSeqTest(data, conditions, uc, AllParti = NULL, iLabel = 1, sizefactor = 1,
  iter = 50, alpha = 0.4, beta = 0, step1 = 1e-06, step2 = 0.01,
  thre = log(2), sthre = 0.001, filter = 10, stopthre = 0.001, nequal = 2)

Arguments

data	A data matrix contains expression values for each transcript (gene or isoform level). In which rows should be transcripts and columns should be samples. For single cell data, normalized counts are required
conditions	condition label for samples
uc	number of unceratin positions, unit level
AllParti	user specified set of partitions
iLabel	label for isoform, indicating how beta are shared among units
sizefactor	The normalization factors. It should be a vector with lane specific numbers (the length of the vector should be the same as the number of samples, with the same order as the columns of Data).
iter	maximum iteration step of EM
alpha	start value of hyper parameter alpha
beta	start value of hyper parameter beta
step1	stepsize for gradient ascent of alpha
step2	stepsize for gradietn ascent of beta
thre	threshold for determining the state of a position
sthre	shrinkage threshold for iterative pruning during the EM updates
filter	filterthreshold for low expression units
stopthre	stopping threshold for EM
nequal	when there is a chain of equal states with the number of equal states bigger than nequal, equalhandle algorithm will be used to further checking the homogeneity between the group means

Value

a list containing selected DE patterns and their posterior probabilities, values for alpha and beta, some moments of the data

wiscstatman/EBSeq documentation built on June 3, 2023, 7:34 a.m.