Description Usage Arguments Details Value Author(s) Examples
Import gene expression data set into R and reformat it to the form required for other functions in this package.
1 2 |
file.name |
a character string of the name of the file to be read. See details. |
name |
The name of the Study object returned |
dtype |
The data type of the dataset (should be one of DTYPE.all) |
clinical.file |
if there is a clinical file containing clinical data relevent to the dataset. |
log |
logical. Specify whether the gene expressions need to
be log2-transformed. The default is |
sep |
the field separator character. Values on each line of
the file are separated by this character. If |
quote |
the set of quoting characters. To disable quoting
altogether, use |
header |
a logical value indicating whether the file contains
the names of the variables as its first line. If missing, the
value is determined from the file format: |
The file to be read should be prepared strictly according following format. The first column should be gene ID and the remaining columns should be the gene expressions for samples. The first row should be sample names and the remaining rows should be gene expression profiles for the samples.
A Study object
Lin Wang, Schwannden Kuo
1 2 3 4 5 6 7 8 9 10 11 | data(study.eg)
data(preproc.option)
write.csv(study.eg@datasets[[1]], file="expr.csv")
write.csv(study.eg@clinicals[[1]], file="clinical.csv")
# Simply read expression data and append clinical data later
study <- ReadExpr(file.name="expr.csv", name="test", dtype=DTYPE.microarray)
clinical <- ReadClinical(file.name="clinical.csv")
study <- setClinical(study, list(clinical))
# Read expression and clinical data
study <- ReadExpr(file.name="expr.csv", name="test", dtype=DTYPE.microarray,
clinical.file="clinical.csv")
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