ReadqPCR (version 1.18.0)

merge: Generic Function for Merging eSet and AnnotatedDataFrame

Description

Generic function for the merging an eSet and an AnnotatedDataFrame; that is, the informatiton given in the AnnotatedDataFrame is merged into the appropriate slot of the given eSet. This can be slot phenoData (default), featureData, or protocolData.

Usage

merge(x, y, ...)
"merge"(x, y, eSet.slot = "phenoData",  by = intersect(names(pData(x)), names(pData(y))), by.x = by, by.y = by,  all = FALSE, all.x = all, all.y = all, sort = FALSE, suffixes = c(".x",".y"),  incomparables = NULL, ...)
"merge"(x, y, eSet.slot = "phenoData",  by = intersect(names(pData(x)), names(pData(y))), by.x = by, by.y = by,  all = FALSE, all.x = all, all.y = all, sort = FALSE, suffixes = c(".x",".y"),  incomparables = NULL, ...)

Arguments

x

object of class eSet or AnnotatedDataFrame

y

object of class eSet or AnnotatedDataFrame

eSet.slot

name of the slot of the given eSet which is merged with the given AnnotatedDataFrame. This can be "phenoData" (default), "featureData", or "protocolData"

by

specifications of the columns used for merging.

by.x

specifications of the columns used for merging.

by.y

specifications of the columns used for merging.

all

logical; all = L is shorthand for all.x = L and all.y = L, where L is either TRUE or FALSE.

all.x

logical; if TRUE, then extra rows will be added to the output, one for each row in x that has no matching row in y. These rows will have NAs in those columns that are usually filled with values from y. The default is FALSE, so that only rows with data from both x and y are included in the output.

all.y

logical; analogous to all.x.

sort

logical. Should the result be sorted on the by columns?

suffixes

a character vector of length 2 specifying the suffixes to be used for making unique the names of columns in the result which not used for merging (appearing in by etc).

incomparables

values which cannot be matched. See match.

...

additional arguments to be passed to or from methods.

Value

"CyclesSet".

Methods

x = "eSet", y = "AnnotatedDataFrame":

merge y into specified slot of x.

x = "AnnotatedDataFrame", y = "eSet":

merge x into specified slot of y.

Details

For details on the arguments see merge.

See Also

merge, eSet

Examples

  path <- system.file("exData", package = "ReadqPCR")
  
  LC480.example <- file.path(path, "LC480_Example.txt")
  ## Read in the raw qPCR data from file "LC480_Example.txt"
  ## with maximum cycle to be read in the values is 45 (default).
  cycData <- read.LC480(file = LC480.example)

  LC480.SamInfo <- file.path(path, "LC480_Example_SampleInfo.txt")
  # Read in the sample information data from file "LC480_Example_SampleInfo.txt". 
  samInfo <- read.LC480SampleInfo(LC480.SamInfo)

  cycData1 <- merge(cycData, samInfo)