SNAGEE (version 1.6.0)

qualSample: Quality of samples in a study

Description

Calculate the relative quality of all samples from a study.

Usage

qualSample(data,mode="complete",cc=NULL,multicore=FALSE)

Arguments

data

The study data. If an Eset, toSnageeFormat is called on it. Otherwise, must be a list with fields 'genes' containing the vector of gene IDs (from Entrez) and 'data' containing the gene expression data.

mode

Which gene-gene correlation matrix should be used. Can be 'complete' (using all platforms) or 'woAffy' (without the Affy platforms).

cc

Can be used if wishing to use a custom gene-gene correlation matrix. Must be a list with fields 'g' containing the gene IDs and 'cc' containing the (upper triangular part of the) correlations.

multicore

Should the parallel version be used? This is based on the parallel package, if that package cannot be loaded it will fall back on single core, with a warning.

Details

The function calculates the quality of all samples in a study. Lower values are of lower quality. The numerical values of the study (the 'data' field) should be in log-scale, and normalized. It is recommended to used medpolish on the data. Each gene should only appear once in the gene list. Duplicated genes must be merged before using the function. Non-finite values should also be removed first (using the impute package for instance).

See Also

SNAGEE, qualStudy, toSnageeFormat

Examples

# Get the list of genes
geneList = getCC()$g;
# Create a random data set
d=list(genes=geneList, data=matrix(rnorm(length(geneList)*50),ncol=50));
# And calculate the quality of the samples (they are all about the same)
qualSample(d);