create_sample_gene_matrix: Create a sample by gene matrix of normalized count values

In Bio-Core/BioCore.CAMs: BioCore Clinicall Aggressive Meningiomas (CAMs) R Package

Description

A function for creating a gene by sample matrix containing normalized counts. The expected input is a dataframe with gene_id, sample and fpkm counts.

Usage

create_sample_gene_matrix(data = NULL, genes = NULL, samples = NULL)

Arguments

data	Dataframe containing gene_id, sample and fpkm. (required)
genes	A vector of gene names to filter (optional, default: NULL)
samples	A vector of sample names to subset (optional, default: NULL)

Value

Returns a dataframe containing samples as columns and gene names as rows.

Author(s)

Richard J. de Borja <[e-mail]

Examples

  data <- data.frame(
    gene_id=c("TP53", "ATK1", "NF2", "TP53", "ATK1", "NF2","TP53", "ATK1", "NF2"),
    sample=c("S1", "S1", "S1", "S2", "S2", "S2", "S3", "S3", "S3"),
    fpkm=c(1.06, 2.4, 2.3, 1.52, 1.33, 1.4, 2.7, 2.1, 8.2))
  data$gene_id <- as.character(data$gene_id)
  data$sample <- as.character(data$sample)
  out_matrix <- create_sample_gene_matrix(
    data=data
  )

Bio-Core/BioCore.CAMs documentation built on May 30, 2019, 6:10 p.m.