table1: table1 - a function to generate a Table 1 figure

Description Usage Arguments

Description

This function allows you to generate a demographics table breaking down the provided characteristics into the groups present in groupChar and optionally to perform tests to determine the differences between groups. This table can be saved to CSV optionally as well.

Usage

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table1(eSet, groupChar, characteristics, groupNames = NULL, printN = T,
  saveResultsCSV = F, filename = "tempTable1.csv", testGroupDiffs = F,
  factorTest = fisher.test, numericTest = aov, userFuncs = NULL)

Arguments

eSet

Either an expression set object or data.frame demographics table

groupChar

The trait (a column name) from the eSet object; each factor level is assumed to be a group that will be represented in the table as a new column

characteristics

The character vector of traits to summarize in the table

groupNames

[optional] User can define the names to be printed in the table, replacing the levels in the groupChar factor

printN

whether or not to add a row at the top of each column with the total number of samples present in that group

saveResultsCSV

Defaults to FALSE; whether to save the table to a csv file

filename

Defaults to tempTable1.csv; filename defining where to save the table

testGroupDiffs

Defaults to FALSE; whether or not to test the group differences on each characteristic; factors tested by fisher and numerics by aov

factorTest

- not implemented yet; Defaults to fisher.test; test used to determine group differences by factor characteristics

numericTest

- not implemented yet; Defaults to aov; test used to determine group differences by numeric characteristics

userFuncs

- not implemented yet table1(eSet=expressionSet, groupChar="CancerStatus", characteristics=c("Smoking", "Sex", "Pack Years"))


SPIRBURG-inc/tableONE documentation built on May 9, 2019, 11:42 a.m.