AskoStats: AskoStats

In askomics/askoR: askoR - Differential Expresion Analysis using edgeR

AskoStats

Description

Based on result contained in "glm_test":

• print summary result of differential expression analysis

• format all results in tabulate out file followed parameters given

• plot heatmap of top differential expressed genes

Create one file by contrast, each file contains for each genes: fold-change and log fold-change values, PValue, Expression, Significance, logCPM, LR, FDR and significance value for each condition/context. By default, LR and logCPM were not displayed, you can switch this parametres to TRUE for display.

Usage

AskoStats(glm_test, fit, contrast, ASKOlist, dge, parameters)

Arguments

glm_test,	tests for one or more coefficients in the linear model (likelihood ratio tests or empirical Bayes quasi-likelihood F-tests).
fit,	fitted linear model object.
contrast,	coefficient/contrast names tested.
ASKOlist,	list of data.frame contain condition, contrast and context informations made by asko3c.
dge,	large DGEList with normalized counts by GEnorm function.
parameters,	list that contains all arguments charged in Asko_start.

Value

none

Examples

## Not run: 
    AskoStats(glm_test, fit, contrast, ASKOlist, dge, parameters)

## End(Not run)

askomics/askoR documentation built on Feb. 4, 2023, 5 a.m.