preprocessedLoader {macat} | R Documentation |
This function reads expression data either from a saved R-file (.RData,.rda), or from a tab-separated text-file (.xls). For building a MACAT-list structure from objects in your workspace, you can either use this function or the convenience wrapper 'buildMACAT'.
preprocessedLoader(rdatafile, chip, labels = NULL, rdafile = TRUE, tabfile = FALSE, labelfile = FALSE)
rdatafile |
Complete name of the expression data file, or the expression matrix |
chip |
Identifier of the used microarray. To date only commercial Affymetrix microarrays are supported by MACAT |
labels |
Classlabels of the samples, vector of same length as number of columns in expression matrix; alternatively complete name of textfile with one label per line |
rdafile |
Logical; is first argument a saved R-file? |
tabfile |
Logical; is first argument a tab-separated text file? |
labelfile |
Logical; is third argument a file with one label per line? |
List of class 'MACATData' with 6 components:
geneName |
Identifiers of genes/probe sets in expression data |
geneLocation |
Location of genes on their chromosome as distance from 5'end in base pairs Negative numbers denote genes on the antisense strand. |
chromosome |
Chromosome of the respective gene. Components 'geneName', 'geneLocation', and 'chromosome' are in the same order. |
expr |
expression matrix with rows = genes and columns = samples/patients |
labels |
(disease) subtype of each sample, has length = number of columns of expression matrix |
chip |
Identifier for Microarray used for the experiments |
To date MACAT can only work with commercial Affymetrix microarrays, denoted by one the following identifiers: hu6800, hgu95av2, hgu95b, hgu95c, hgu95d, hgu95e, hgu133a, hgu133b, mgu74av2, mgu74bv2, mgu74c, moe430a, moe430b, rae230a, rae230b, rgu34a, rgu34b, rgu34c
MACAT development team
buildMACAT
,read.table
,stjd
,stjude
in package 'stjudem'
## Not run: # assume you have your HG-U95Av2 expression values in a # tab-separated text file, called 'foo.txt' mydata <- preprocessedLoader("foo.txt","hgu95av2",rdafile=FALSE,tabfile=TRUE) ## End(Not run)