countToTpm: Convert count to Tpm

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

Convert count to Tpm

Description

Convert count to Tpm

Usage

countToTpm(counts_matrix, keyType = "SYMBOL", gene_cov)

Arguments

counts_matrix	a matrix, colnames of counts_matrix are sample name, rownames of counts_matrix are gene symbols
keyType	keyType, one of keytypes(org.Hs.eg.db).
gene_cov	data.frame of two column, the first column is gene length, the second column is gene GC content

Value

a matrix

Examples

data(gene_cov)
lung_squ_count2 <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9), ncol = 3)
rownames(lung_squ_count2) <- c("DISC1", "TCOF1", "SPPL3")
colnames(lung_squ_count2) <- c("sample1", "sample2", "sample3")
result <- countToTpm(lung_squ_count2,
    keyType = "SYMBOL",
    gene_cov = gene_cov
)

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