differential_array: Differential analysis of Microarray data

In huerqiang/GeoTcgaData: Processing Various Types of Data on GEO and TCGA

Differential analysis of Microarray data

Description

Differential analysis of Microarray data

Usage

differential_array(df, group, method = "limma", adjust.method = "BH")

Arguments

df	data.frame of the omic data, each column is a sample, and each row is a gene.
group	a vector, group of samples.
method	method to do differential analysis, one of "limma", "ttest", "wilcox".
adjust.method	adjust.method, one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none".

Value

data.frame

Examples

library(GeoTcgaData)
library(data.table)
# Use real GEO data as example
arrayData <- read.table("GSE54807_series_matrix.txt.gz",
    sep = "\t", header = TRUE,
        fill=TRUE, comment.char = "!", check.names=FALSE)
gpl <- fread("GPL6244-17930.txt", sep = "\t", header = TRUE)
gpl <- gpl[, c("ID", "gene_assignment")]
class(gpl) <- "data.frame"

for (i in seq_len(nrow(gpl))) {
        aa <- strsplit(gpl[i, 2], " // ")[[1]][5]
        gpl[i, 2] <- as.character(strsplit(aa, " /// ")[[1]][1])
}
gpl[,1] <- as.character(gpl[,1])
arrayData[, 1] <- as.character(arrayData[, 1])
rownames(gpl) <- gpl[, 1]
arrayData[, 1] <- gpl[arrayData[, 1], 2]


arrayData <- repRemove(arrayData," /// ")

# Remove rows that do not correspond to genes
arrayData <- arrayData[!is.na(arrayData[, 1]), ]
arrayData <- arrayData[!arrayData[, 1] == "", ]
arrayData <- arrayData[!arrayData[, 1] == "---", ]


arrayData <- arrayData[order(arrayData[, 1]), ]
arrayData <- gene_ave(arrayData, 1)

keep <- apply(arrayData, 1, function(x) sum(x < 1) < (length(x)/2))
arrayData <- arrayData[keep, ]

group <- c(rep("group1", 12), rep("group2", 12))
result <- differential_array(df = arrayData, group = group)

# Use random data as example
arrayData <- matrix(runif(200), 25, 8)
rownames(arrayData) <- paste0("gene", 1:25)
colnames(arrayData) <- paste0("sample", 1:8)
group <- c(rep("group1", 4), rep("group2", 4))
names(group) <- colnames(arrayData)
result <- differential_array(df = arrayData, group = group)

huerqiang/GeoTcgaData documentation built on March 21, 2024, 1:42 a.m.