pheno.list: List to describe the covariate and outcome data

In ARTP: Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product

Description

The list to describe the covariate and outcome data for runPermutations

Format

The format is a list:

file

Covariate data file. This file must have variable names, two of which being an id variable and a response variable (see id.var and response.var). No default.

id.var

Name of the id variable. No default.

response.var

Name of the response variable. For logistic regression analyses, this variable must be coded as 0 (control) and 1 (case). No default.

main.vars

Character vector of variables names for variables in file that will be included in the model as main effects. The default is NULL.

delimiter

The delimiter in file. The default is "".

in.miss

Vector of character strings to define the missing values. This option corresponds to the option na.strings in read.table. The default is "NA".

Details

In this list, file, id.var, and response.var must be specified. The variable id.var is the link between the covariate data and the genotype data. For each subject id, there must be the same subject id in the genotype data for that subject to be included in tha analysis.
Missing data: If any of the variables defined in main.vars, int.vars, or response.var contain missing values, then those subjects will be removed from the covariate and outcome data. After the subjects with missing values are removed, the subject ids are matched with the genotype data.

ARTP documentation built on May 2, 2019, 6:51 a.m.