AskoStats: AskoStats

In askomics/askoR: Differential Expression 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, data_list, 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.
data_list	list contain all data and metadata (DGEList, samples descriptions, contrast, design and annotations).
parameters	list that contains all arguments charged in Asko_start.

Value

none

Note

Remember to read the Wiki section in https://github.com/askomics/askoR/wiki

Examples

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

## End(Not run)

askomics/askoR documentation built on Jan. 17, 2025, 6:23 p.m.