Description Usage Arguments Value Examples
Returns z-score matrix for a given GEO data set. The z-scores are calculated for each gene in each sample using the mean and sd over provided control samples.
1 2 | get.z.matrix(expr, sample.mapping, states.control = NULL,
states.case = NULL, method = "mean", out.file = NULL)
|
expr |
Expression matrix (genes vs samples), tab separated. |
sample.mapping |
Sample - condition mapping. |
states.control |
Label of control (background) samples. If NULL sample.mapping is assumed to include the following types: "case" "control". |
states.case |
Label of case (disease) samples. |
method |
Method to calculate the z score, defaults to mean and sd, use median for med and mad. |
out.file |
Output file for writing z score matrix. |
Data frame containing z-scores
1 2 3 4 5 6 | gds.data = fetch.expression.data("GDS4966", do.log2=F, probe.conversion="Gene ID")
expr = gds.data$expr
sample.mapping = gds.data$sample.mapping
z = get.z.matrix(expr, sample.mapping,
states.control = c("healthy donor"),
states.case = c("tuberculosis", "latent tuberculosis infection"))
|
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