read_sampleData: Read in a sample data table.

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

Read in a sample data table.

Description

Read in a .txt or .csv file containing sample names, group identifiers, replicate identifiers, and any other sample data. Sample names must be in the first column and must correspond with sample names in the count data file(s).

Usage

read_sampleData(dat, file.name, idCol = NULL, groupCol, replicateCol = NULL)

Arguments

dat	expression data, read in by read_merge_rcc or read.delim
file.name	the path/name of the .txt or .csv file
idCol	the column name of the sample identifiers in the sample table, which should correspond to the column names in the count table (default NULL: will assume the first column contains the sample identifiers).
groupCol	the column name of the group identifiers.
replicateCol	the column name of the replicate identifiers (default NULL). Multiple replicates of the same sample will have the same value in this column.

Value

The list with the expression data, now combined with the sample information

Examples

example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube")
sample_info <- system.file("extdata", "GSE117751_sample_data.csv", 
                           package = "NanoTube")

dat <- read_merge_rcc(list.files(example_data, full.names = TRUE))

# Merge expression data with sample info
dat <- read_sampleData(dat, file.name = sample_info,
                       groupCol = "Sample_Diagnosis")

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.