integIRTy (version 1.0.8)

dichotomize: 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"), ...)

Value

Abinary matrix of the same dimension as input mat.

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.

Author

Pan Tong ([e-mail]), Kevin R Coombes ([e-mail])

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')