detectReplicas {arrayMagic}R Documentation

detectReplicas

Description

The function returns for each unique item all corresponding indexes.

Usage

detectReplicas(arrayDescription, spotIdentifier = "ID", identifiersToBeSkipped = NULL, verbose = TRUE)

Arguments

arrayDescription an object of class data.frame which contains a column named as spotIdentifier; required; default missing
spotIdentifier character string; required; default: "ID"
identifiersToBeSkipped vector of character strings; required; default: NULL; items of the column spotIdentifier for which no replica detection takes place
verbose logical; required; default: TRUE

Value

A list which contains nrOfReplicas and spotReplicas. nrOfReplicas: one integer characterizing the number of spot replicas given for each identifier if existing or otherwise NA. spotReplicas: a list of the length of the unique identifiers where each element contains a vector of indexes corresponding to the given identifier (i.e. the name of the list element) otherwise NA.

Author(s)

Andreas Buness <a.buness@dkfz.de>

Examples


aD <- data.frame(ID=c("z", "x", "x", "x", "y", "z", "z", "y", "y"))
re <- detectReplicas(aD, identifiersToBeSkipped = c("Blank", "Control1", "Control2"))
stopifnot(re[["nrOfReplicas"]] == 3 )
stopifnot( re$spotReplicas[["z"]] == c(1,6,7) )
stopifnot( re$spotReplicas[["x"]] == c(2,3,4) )
stopifnot( re$spotReplicas[["y"]] == c(5,8,9) )

aD <- data.frame(ID=c("Blank", "Control1", "Blank", "Control2"))
re <- detectReplicas(aD, identifiersToBeSkipped = c("Blank", "Control1", "Control2"))
stopifnot(is.na(re[["nrOfReplicas"]]))

 
  

[Package arrayMagic version 1.8.0 Index]