prep.gsda {GSDA} | R Documentation |
A function to prepare omic data, clinical data and variable set into an ordered matched format for GSDA analysis.
prep.gsda(data.mtx, clin.data, vset.data = NULL)
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). |
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.
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. |
Xueyuan Cao xcao12@uthsc.edu and Stanley Pounds stanley.pounds@stjude.org
Cao X and Pounds S (2021) Gene-Set Distance Associations (GSDA): A Powerful Tool for Gene-Set Association Analysis.
data(target.aml.clin)
data(target.aml.expr)
data(kegg.ml.gsets)
gsdaprep=prep.gsda(target.aml.expr,
target.aml.clin,
kegg.ml.gsets)