readData: Creating an object of eSet class

In SoniaTC/NOISeq: Exploratory analysis and differential expression for RNA-seq data

Description

This function is to create an object of eSet class to be used by NOISeq functions from matrix or data.frame R objects.

Usage

readData(data, factors, length = NULL, biotype = NULL, chromosome = NULL, gc = NULL)
addData(data, length = NULL, biotype = NULL, chromosome = NULL, factors = NULL, gc = NULL)

Arguments

data	Matrix or data.frame containing the counts (or expression data) for each feature and sample. Features must be in rows and samples must be in columns.
factors	A data.frame containing the experimental condition or group for each sample (columns in the data object).
biotype	Optional argument.Vector, matrix or data.frame containing the biological group (biotype) for each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the biotypes of the features in the second. If it only has one column containing the biotypes, the rownames of the object must be the feature names or ids.
chromosome	Optional argument. A matrix or data.frame containing the chromosome, start position and end position of each feature. The rownames must be the feature names or ids with the same type of identifier used in data.
gc	Optional argument.Vector, matrix or data.frame containing the GC content of each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the GC content of the features in the second. If it only has one column containing the GC content, the rownames of the object must be the feature names or ids.
length	Optional argument.Vector, matrix or data.frame containing the length of each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the length of the features in the second. If it only has one column containing the length, the rownames of the object must be the feature names or ids.

Value

It returns an object of eSet class myCounts with all the information defined and ready to be used.

Author(s)

Sonia Tarazona

References

Marioni, J.C. and Mason, C.E. and Mane, S.M. and Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18: 1509–1517.

Examples

# Load an object containing the information explained above
data(Marioni)

# Create the object with the data        
mydata <- readData(data=mycounts, biotype=mybiotypes, chromosome=mychroms, factors=myfactors)

# Add length annotation to the existing data object
mydata <- addData(mydata, length=mylength)

SoniaTC/NOISeq documentation built on July 28, 2020, 6:31 p.m.