LfcTest: Hypothesis test to detect log fold change

In cuiyingbeicheng/BEDFC: Log fold change detection based on an empirical bayesian method.

Description

The procedure to conduct hypothesis test to detect if the ratio of $mu^g_2$ and $mu^g_1$ (i.e., fold change) is within or outside a region of interest.

Usage

LfcTest(Y, cis.chr = cis.chr, cis.null.lfc = cis.null.lfc, trans.null.lfc = trans.null.lfc)

Arguments

Y	Log fold change with base 2
cis.chr	Altered chromosome
cis.null.lfc	Null log fold change for the genes located on treated chromosome
trans.null.lfc	Null log fold change for the genes located on untreated chromosome

Details

A complete pipeline to conduct the hypothesis testing:

Step1:Parameter estimation;

Step2:Calculate test statistic;

Step3:Detect log fold change based on the statistics.

Value

cis.high	Summary the statistics of highly expressed genes located on the treated chromosome
cis.lower	Summary the statistics of lowly expressed genes located on the treated chromosome
cis.null	Summary the statistics of the non-differential genes located on the treated chromosome
trans.high	Summary the statistics of highly expressed genes located on the untreated chromosom
trans.lower	Summary the statistics of lowly expressed genes located on the untreated chromosome
trans.null	Summary the statistics of the non-differential genes located on the untreated chromosome
sumStat	Summary the number of genes in each gene group

cuiyingbeicheng/BEDFC documentation built on Nov. 8, 2019, 12:34 a.m.