raw.pvalues | R Documentation |
Calculates for each gene expression, the Fisher test statistics and the corresponding p-value for H0: the gene expression does not depend on the experimental condition in a model with possible covariates.
raw.pvalues(data, x = 1, test = x[1])
data |
'FAMTdata' object, see |
x |
Column number(s) corresponding to the experimental condition and the optional covariates (1 by default) in the 'covariates' data frame. |
test |
Column number corresponding to the experimental condition (x[1] by default) of interest in the multiple testing procedure. |
pval |
Vector containing the p-values |
test |
Vector containing the F statistics |
resdf |
Residual degrees of freedom |
David Causeur
as.FAMTdata
data(expression) data(covariates) data(annotations) # Create the 'FAMTdata' ############################################ chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2) # 'FAMTdata' summary summaryFAMT(chicken) # Calculation of classical p-values ############################################ # test on the 6th covariate: rawpval = raw.pvalues(chicken,x=6) hist(rawpval$pval) # with a supplementary covariate (third column of the covariates data frame) ## Not run: rawpval = raw.pvalues(chicken,x=c(3,6),test=6) ## Not run: hist(rawpval$pval)
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