merge: Generic Function for Merging eSet and AnnotatedDataFrame
In ReadqPCR: Read qPCR data

Description Usage Arguments Details Value Methods Author(s) See Also Examples

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.

merge(x, y, ...)
## S4 method for signature 'eSet,AnnotatedDataFrame'
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, ...)
## S4 method for signature 'AnnotatedDataFrame,eSet'
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, ...)

`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.

For details on the arguments see merge.

Object of class "CyclesSet".

x = "eSet", y = "AnnotatedDataFrame":: merge y into specified slot of x.
x = "AnnotatedDataFrame", y = "eSet":: merge x into specified slot of y.

Nor Izayu Abdul Rahman, Matthias Kohl Matthias.Kohl@stamats.de

merge, eSet

  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)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

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