make.matches: make.matches: make matches

In mauriziopaul/treatmentResponseDiallel: Package For the Analysis of Treatment-Response Phenotypes in the Influenza Diallel Project

Description

Makes one or more matches between treated and control mice in the flu diallel based on specified classes and match strategy. In the manuscript, matches do not differ between imputations (same quartets always selected), but imputed phenotype values differ.

Usage

make.matches(data, reps, trt.colname = "Trt", trt.string, ctrl.string, fdir,
  force = TRUE, strategy = c("one-to-one", "two-to-one", "three-to-one",
  "mean")[1], select.phenotype = FALSE, ignore.batch = FALSE,
  ignore.day = TRUE, batch = "Block", matchname = "", ...)

Arguments

data	data set
reps	number of repetitions or matches
trt.colname	treatment column name
trt.string	treated
ctrl.string	control
fdir	file directory
force	logical indicating whether to force matching despite warnings/errors
strategy	this gives the treatment-to-control ratio (one-to-one, two-to-one), or mean match
select.phenotype	logical indicating whether to select a specific phenotype
ignore.batch	logical indicating whether to match independently of batch (TRUE), or within batch (FALSE)
ignore.day	logical indicating whether to match independently of day assignment (TRUE), or within day assignment (FALSE)
batch	character string giving batch column name
matchname	name of match file
...	additional arguments

Value

returns matched treatment response files

Examples

## This example may take a couple of minutes
data(FluDiData)
write.csv(FluDiData, file="FluDiData.csv")
filename <- "FluDiData.csv"
data <- read.csv("FluDiData.csv")
reps <- 1
trt.string <- "FLU"
ctrl.string <- "MOCK"
fdir <- "." 
strategy <- "mean"
make.matches(data=data, reps=reps, trt.string=trt.string, 
             ctrl.string=ctrl.string, fdir=fdir, strategy=strategy)

mauriziopaul/treatmentResponseDiallel documentation built on May 21, 2019, 1:37 p.m.