FAMT (version 2.6)

summaryFAMT: Summary of a FAMTdata or a FAMTmodel

Description

The function produces summaries of 'FAMTdata' or 'FAMTmodel'. The function involves a specific method depending on the class of the main argument.

If the main argument is a 'FAMTdata' object, the function provides, for the 'expression file', the number of tests (which corresponds to the number of genes or rows), the sample size (which is the number of arrays or columns). The function provides classical summaries for 'covariates' and 'annotations' data (see summary in FAMT-package).

If the argument is a 'FAMTmodel', the function provides the numbers of rejected genes using classical and FAMT analyses, the annotation characteristics of significant genes, and the estimated proportion of true null hypotheses.

Usage

summaryFAMT(obj, pi0 = NULL, alpha = 0.15, info = c("ID", "Name"))

Arguments

obj

'FAMTdata' or 'FAMTmodel', see also as.FAMTdata, modelFAMT

pi0

Proportion of tests under H0. NULL, by default, it is estimated.

alpha

Type I levels for the control of the false discovery rate (0.15 by default) if the first argument is 'FAMTmodel' (it can be a single value or a vector).

info

Names of the columns containing the genes identification and array names in the original data frames, necessary if the first argument is 'FAMTmodel'

Value

If the argument is a 'FAMTdata': a list with components expression:

expression$'Number of tests'

Number of genes

expression$'Sample size'

Number of arrays

covariates

Classical summary of covariates

annotations

Classical summary of annotations

If the argument is a 'FAMTmodel':

nbreject

Matrix giving the numbers of rejected genes with the classical analysis and with the FAMT analysis for the given Type I levels alpha.

DE

Identification of the significant genes by their annotations.

pi0

Estimation of the proportion of true null hypotheses, estimated with the "smoother" method, see pi0FAMT.

See Also

as.FAMTdata, modelFAMT

Examples

# NOT RUN {
## Reading 'FAMTdata'
data(expression)
data(covariates)
data(annotations)
chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2)

## Summary of a 'FAMTdata'
#############################################
summaryFAMT(chicken)

## Summary of a 'FAMTmodel'
#############################################
# FAMT complete multiple testing procedure 
model = modelFAMT(chicken,x=c(3,6),test=6,nbf=3)
summaryFAMT(model)
# }