read.mir(files=NULL, source="agilent.median", path=NULL, ext=NULL, names=NULL, columns=NULL, other.columns=NULL, annotation=NULL, green.only=TRUE, wt.fun=NULL, verbose=TRUE, sep="\t", quote=NULL, remove.ctrl=TRUE,...)
FileName
.
If omitted, then all files with extension ext
in the specified directory will be read in alphabetical order."agilent.median"
, "agilent.mean"
.removeExt(files)
.R
, G
, Rb
and Gb
giving the column names to be used for red and green foreground and background or, in the case of Imagene data, a list with fields f
and b
.
For single channel data, the fields are usually E
and Eb
.
This argument is optional if source
is specified, otherwise it is required.source
, should the
green (Cy3) channel only be read, or are both red and green
required?. Standard Agilent MIR data have only one channel so
defaults to TRUE
.TRUE
to report each time a file is readTRUE
control probes will not be readread.table
FileName
giving the names of the files read, with column Sample
giving the names of the samplse.Background
,
Normalization
, is.log
, Summarization
indicate
which pre-processing step has beendone.columns
argument (This will work if the column names are unique and if there
are no incomplete rows in the file after the last line of data. Header
lines are ok, if appropriately skipped).
The function is a simple wrapper for
"read.maimages"
in limma
package so it shares all its features (though right now the input
source is restricted to agilent type file).
The argument files
should be a matrix with two columns at
least. One column should contain the names of the samples and the other
column should contain names of files containing intensity data.
The argument other.columns
allows arbitrary columns of the image
analysis output files to be reserved in the data object. These become
matrices in the 'other' component.
read.mir
is based on "read.table"
in the base
package and modified from "read.maimages"
in the limma
package.# Read all intensity files from current working directory
## Not run:
# dir.files <- system.file("extdata", package="LVSmiRNA")
# taqman.data <- read.table(file.path(dir.files,"Comparison_Array.txt"),header=TRUE,as.is=TRUE)
# MIR <- read.mir(taqman.data)
# ## End(Not run)
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