prep.gsda {GSDA}

GSDA Data Preparation

Description

A function to prepare omic data, clinical data and variable set into an ordered matched format for GSDA analysis.

Usage

prep.gsda(data.mtx, clin.data, vset.data = NULL)

Arguments

data.mtx

Numeric data matrix with column names giving subject identifiers.

clin.data

Data.frame with column named "ID" with subject identifiers matching column names of data.mtx.

vset.data

data.frame of variable-set assignments with columns named "vID" for variable identifier and "vset" for name or identifier of a variable set (gene-set).

Details

The gsda function uses prep.gsda to prepare the omic data matrix, clinical dataframe and variable set (gene set) into ordered and matched format, which is then used for GSDA analysis.

Value

A list with the following components:

omic.data

data matrix with columns in the same order as clin.data$ID.

clin.data

data.frame with ID column in same order as columns of omic.data.

vset.data

variable set ordered by name of variable set.

vset.index

simple data.frame showing first and last row of vset.data for each variable set.

Author(s)

Xueyuan Cao [e-mail] and Stanley Pounds [e-mail]

References

Cao X and Pounds S (2021) Gene-Set Distance Associations (GSDA): A Powerful Tool for Gene-Set Association Analysis.

See Also

gsda

Examples

data(target.aml.clin)
data(target.aml.expr)
data(kegg.ml.gsets)
gsdaprep=prep.gsda(target.aml.expr,
         target.aml.clin,
         kegg.ml.gsets)