differential_SNP_GEO: Do difference analysis of SNP data downloaded from GEO

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

Do difference analysis of SNP data downloaded from GEO

Description

Do difference analysis of SNP data downloaded from GEO

Usage

differential_SNP_GEO(snpData, sampleGroup, method = "Chisquare")

Arguments

snpData	data.frame of SNP data downloaded from GEO
sampleGroup	vector of sample group
method	one of "Chisquare", "fisher", and "CATT"(Cochran-Armitage trend test)

Value

data.frame

Examples

file1 <- read.table("GSE66903_series_matrix.txt.gz",
    fill=TRUE, comment.char="!", header = TRUE)
rownames(file1) <- file1[, 1]
snpData <- file1[, -1]
sampleGroup <- sample(c("A", "B"), ncol(snpData ), replace = TRUE)
names(sampleGroup) <- colnames(snpData)
snpData <- SNP_QC(snpData)
sampleGroup <- sample(c("A", "B"), ncol(snpData ), replace = TRUE)
result1 <- differential_SNP_GEO(snpData = snpData,
    sampleGroup = sampleGroup, method = "Chisquare")

# use demo data
snpDf <- matrix(sample(c("AA", "Aa", "aa"), 100, replace = TRUE), 10, 10)
snpDf <- as.data.frame(snpDf)
sampleGroup <- sample(c("A", "B"), 10, replace = TRUE)
result <- differential_SNP_GEO(snpDf, sampleGroup, method = "fisher")

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