| dichotomize {integIRTy} | R Documentation |
A wrapper that is able to dichotomize expression, methylation and CN data
Description
This function provides a common interface for the user so that data dichotomization can be done easily.
Usage
dichotomize(mat, matCtr, assayType = c("Expr", "Methy", "CN"), ...)
Arguments
mat |
A matrix, either expression, methylation or CN |
matCtr |
A matrix corresponding to normal controls. |
assayType |
A character string specifying the assay type. It can only be any of "Expr", "Methy", "CN". For assays none of these types, the program will quite. To run intIRT, the user can manually dichotomize the data and feed them into intIRTeasyRun function. |
... |
Additional parameters to be passed to the specific dichotomization function. |
Value
Abinary matrix of the same dimension as input mat.
Author(s)
Pan Tong (nickytong@gmail.com), Kevin R Coombes (krc@silicovore.com)
References
Tong P, Coombes KR. integIRTy: a method to identify altered genes in cancer accounting for multiple mechanisms of regulation using item response theory. Bioinformatics, 2012 Nov 15; 28(22):2861–9.
See Also
dichotomizeCN, dichotomizeExpr, dichotomizeMethy
Examples
data(OV)
binDat_expr <- dichotomize(Expr_T[1:20, ], Expr_N[1:20, ], assayType='Expr')
binDat_methy <- dichotomize(Methy_T[1:20, ], Methy_N[1:20, ], assayType='Methy')