ddCt (version 1.28.0)

SDMFrame: Read an SDM file

Description

Read an SDM file: Data Output File for SDS, Version 2.1

Usage

SDMFrame(file) readSDM(file)

Arguments

file

Character vector of filenames

Value

SDMFrame

Details

This function reads the data given in the colums 'Detector','Sample' and 'Ct' of the specified SDM output file(s) and stores them as a data.frame. An additional column including the respective filename is added.

This function is a wrapper for the SDMFrame constructor

Examples

## read a SDM file
sampdat <- SDMFrame(system.file("extdata", "Experiment1.txt",
                                package="ddCt"))
## you can also write 
## sampdat <- new("SDMFrame",system.file("extdata", "Experiment1.txt",
##                                       package="ddCt"))

## or with
## sampdat <- readSDM(system.file("extdata", "Experiment1.txt",
##                                package="ddCt"))

## use the getter methods
sampleNames(sampdat)

## or the overloaded primitive accessors
sampdat[1:3,"Sample"]

## see all unique samples
uniqueSampleNames(sampdat)

## replace all sample names 'Sample1' and 'Sample2' in sampdat
## with 'NewSample1' and 'NewSample2'
uniqueSampleNames(sampdat,c("Sample1","Sample2")) <- c("NewSample1","NewSample2")
uniqueSampleNames(sampdat)

## or use this syntax to replace the gene names
uniqueDetectorNames(sampdat) <- c(Gene1="NewGene1", Gene2="NewGene2")
uniqueDetectorNames(sampdat)