DELocal: Finds differentially expressed genes by comparing neighboring...

In dasroy/DELocal: Identifies differentially expressed genes with respect to other local genes

Finds differentially expressed genes by comparing neighboring genes

Description

Finds differentially expressed genes by comparing neighboring genes

Usage

DELocal(
  pSmrExpt,
  nearest_neighbours,
  pDesign,
  pValue_cut = 0.05,
  pLogFold_cut = 0
)

Arguments

pSmrExpt	SummarizedExperiment object
nearest_neighbours	How many nearest neighbours within 1 Mb window to evaluate?
pDesign	design formula
pValue_cut	cut off value for adjusted p-value
pLogFold_cut	cut off value for relative log fold change compared to neighbouring genes

Value

A data.frame with top significant genes with the following columns:

relative.logFC: relative logFC compared to neighbouring genes

P.Value: raw p-value

adj.P.Value: adjusted p-value

B: log-odds that the gene is differentially expressed

Examples

count_matrix <- as.matrix(read.table(file = system.file("extdata",
                                                                  "tooth_RNASeq_counts.txt",
                                                                  package = "DELocal")))
colData <- data.frame(condition=gsub("\\..*",x=colnames(count_matrix),
                                     replacement = ""))
gene_location <- read.table(file = system.file("extdata", "gene_location.txt",
                                    package = "DELocal"))
smrExpt <- SummarizedExperiment::SummarizedExperiment(
                                        assays=list(counts=count_matrix),
                                        rowData = gene_location,
                                        colData=colData)
contrast= c("condition","ME13","ME14")
require(dplyr)
x_genes <- SummarizedExperiment::rowData(smrExpt) %>%
      as.data.frame() %>%
      filter(chromosome_name=="X") %>% rownames()
DELocal_result <- DELocal(pSmrExpt = smrExpt[x_genes,],
                         nearest_neighbours = 5, pDesign = ~ condition,
                         pValue_cut = 0.05, pLogFold_cut = 0)

dasroy/DELocal documentation built on Feb. 7, 2024, 9:28 a.m.