readArrays: Read peptide microarray data from GPR files
In katenambiar/pmpa: Peptide Microarray Pre-Processing and Analysis
Description
Usage
Arguments
Value
Description
readArrays is a function used to read in peptide microarray data
from Genepix GPR files (in Axon ATF format). It produces a Bioconductor
MultiSet object with microarray signal intensity data (foreground
intensity, background intensity and other measures for assessing
feature quality) in the assayData slot. A minimal annotation set
is created by recording sample data (sample unique identifier and file name)
in the phenoData slot, and feature data (feature names and ID, and
layout information) in the featureData slot. The scan date and time
for the GPR file (if recorded in the GPR header) is written to the
annnotated data frame in the protocolData slot. Only signal intensity
data from a single wavelength (single colour data) is imported.
Usage
1
2
readArrays(samplename = NULL, filename = NULL, path = NULL,
wavelength = NULL)
Arguments
wavelength
integer value for the scan wavelength
(typically 635 for Cy5 and 532 for Cy3)
files
a data frame with 3 columns:
sampleName - unique identifier for the sample,
fileName - GPR file name and extension,
path - full path or URL to the directory holding the GPR file
Value
an object of class MultiSet
katenambiar/pmpa documentation built on May 20, 2019, 7:41 a.m.
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Description Usage Arguments Value
Description
readArrays is a function used to read in peptide microarray data
from Genepix GPR files (in Axon ATF format). It produces a Bioconductor
MultiSet object with microarray signal intensity data (foreground
intensity, background intensity and other measures for assessing
feature quality) in the assayData slot. A minimal annotation set
is created by recording sample data (sample unique identifier and file name)
in the phenoData slot, and feature data (feature names and ID, and
layout information) in the featureData slot. The scan date and time
for the GPR file (if recorded in the GPR header) is written to the
annnotated data frame in the protocolData slot. Only signal intensity
data from a single wavelength (single colour data) is imported.
Usage
1 2 | readArrays(samplename = NULL, filename = NULL, path = NULL,
wavelength = NULL)
|
Arguments
wavelength |
integer value for the scan wavelength (typically 635 for Cy5 and 532 for Cy3) |
files |
a data frame with 3 columns: sampleName - unique identifier for the sample, fileName - GPR file name and extension, path - full path or URL to the directory holding the GPR file |
Value
an object of class MultiSet
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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