readTSGE: Read and merge a set of files containing gene expression data

In ctsGE: Clustering of Time Series Gene Expression data

Description

Reads and merges a set of text files containing normalized gene expression data

Usage

readTSGE(files, path = NULL, columns = c(1, 2), labels = NULL,
  desc = NULL, ...)

Arguments

files	character vector of filenames, or alternative a named list of tables for each time point.
path	character string giving the directory containing the files. The default is the current working directory.
columns	numeric vector stating which two columns contain the tag names and counts, respectively
labels	character vector giving short names to associate with the libraries.
desc	character vector with genes description (annotation),default to NULL Defaults to the file names.
...	other are passed to read.delim

Details

As input, the ctsGE package expects normalized expression table, where rows are genes and columns are samples Each file is assumed to contained digital gene expression data for one sample (or library), with transcript or gene identifiers in the first column and expression values in the second column. Transcript identifiers are assumed to be unique and not repeated in any one file. By default, the files are assumed to be tab-delimited and to contain column headings. The function forms the union of all transcripts and creates one big table with zeros where necessary. When reading the normalized expression values the function check whether there are rows that their median absolute deviation (MAD) value equal to zero and remove these rows. This step is important in order to continue to the next step of indexing the data. The function will output a message of how many genes were remove.

Value

A list with four objects:

1. expression matrix

2. samples names

3. tags - genes name

4. timePoints - number of time points

Examples

## Read all .txt files from current working directory
data_dir <- system.file("extdata", package = "ctsGE")
files <- dir(path=data_dir,pattern = "\\.xls$")

# reading only 2000 genes
rts <- readTSGE(files, path = data_dir,
 labels = c("0h","6h","12h","24h","48h","72h"), skip = 10625 )

Example output

ctsGE documentation built on Nov. 8, 2020, 11:06 p.m.