loadExpr: Load txt files into matrix or dataframe
In weiyi-bitw/cafr: Attractor Metagenes Finding Algorithm

Description Usage Arguments Details Value Author(s) See Also Examples

Functions to load txt files of gene expression data or clinical data into matrix or dataframe.

1 2	loadExpr(file, sep='\t') loadClin(file, sep='\t')

`file`	File path to the text file, in which first row is the header, first column contains row names.
`sep`	the field separator character. As defined in the `read.table` function.

loadExpr and loadClin use readLines function to process text files, thus bypass some cases where read.table hangs due to warnings caused by the file. It also provides a progress bar for progress monitoring.

loadExpr returns a matrix with expression values. loadClin returns a matrix with text entries. The popular notations for missing values are treated as 'NA' in the matrix.

Wei-Yi Cheng

read.table

# This example requires a Synapse account. It shows how to load expression data and 
# clinical data from Synapse.
## Not run: 
require(synapseClient)
synapseLogin()

# Load TCGA READ IlluminaHiSeq RNASeq data
syn <- loadEntity("syn1446276")
fileName <- file.path(syn$cacheDir, syn$files[[1]])
ge <- loadExpr(fileName)

# Load TCGA READ Clinical_patient file
syn <- loadEntity("syn1446151")
fileName <- file.path(syn$cacheDir, syn$files[[1]])
clnc <- loadClin(fileName)

## End(Not run)