loadCounts: Loading the count table, the Pheno table and vector of class...

In elqumsan/RNAseqMVA: Application of Multivariate Analysis methods to RNA-seq Data

Description

Given a ReCount ID, load the count table, the pheno table and the vector of class labels, prepares and filters the count table, via wrapper runs by sample.

Usage

loadCounts(recountID, parameters, ...)

Arguments

recountID	number of experiment
parameters	list of parameters (supposedly loaded from the yaml configuration file)
...	additional parameters are passed to loadRecountExperiment()

Value

it is returen the two feature types:

1. for the original counts that means implicitly the raw count table before making ang pre-processing proccess.

2. for the filtered count that means implicitly the raw count after made the pre-processing proccess,

• filtered: count table after applying the pre-processing proccess.

Author(s)

Mustafa ABUELQUMSAN and Jacques van Helden

Examples

##############################################
## Load an RNA-seq dataset and merge counts per sample.
# This assumes that the required parameters have been specified
# in the YAML configuration file.
x <- loadCounts( recountID = "SRP048759", parameters = parameters)


## RCurl and XML are Required for recount but not declared in dependencies

elqumsan/RNAseqMVA documentation built on March 10, 2021, 8:10 a.m.