clusteringSummary: Get the annotations used in a NCBI GEO dataset

In spell098/rnaseq_functions2: Contain various functions for rnaseq analysis

Description

Get the annotations used in a NCBI GEO dataset

Usage

clusteringSummary(expr.matrix, pval, names)

Arguments

expr.matrix	A matrix of numeric values. Rows are genes, columns are samples
pval	Alpha value (selected p-value)

Value

A table with all the annotation for a platform

Author(s)

Simon J Pelletier

See Also

fuzzy_clustering , phyper

Examples

expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
pval <- 0.05
summaryClust <- clusteringSummary(expr.matrix,pval)

gset <- getGEO("GSE44593", GSEMatrix =TRUE)
exprset <- gset[[1]]
expr.matrix <- exprs(exprset)
names1 <- get_names(sampleNames(exprset))
groupBy <- "group"
noCluster <- 3
fileContent <- "Expression Set"
names1 <- get_names(expr.matrix)
selectedVariables <- NULL
comparisonsTable <- comparisonsPheno(exprset)[[2]]
namesTable <- comparisonsTable
names2 <- namesSelectedComparisons(namesTable)
summaryClust <- clusteringSummary(expr.matrix,pval,names2)

spell098/rnaseq_functions2 documentation built on May 30, 2019, 7:57 a.m.