gene_filter | R Documentation |
A wrapper of two genefilter functions to filter low expressed and low variability genes (rows). The default settings will keep genes for which 1) at least 33 or above; and 2) ratio of maximal/minimal intensity is at least 2
gene_filter( mtx, proportion = 0.33, average_expression = 10, min_difference = 2 )
mtx |
a matrix of genes (rows) vs. samples (columns), or an ExpressionSet. Required. |
proportion |
a proportion of samples having gene expressed above 'average_expression'. Default - 0.33 |
average_expression |
expression level to be exceeded when calculating 'proportion'. Default - 10 |
min_difference |
expression difference between maximal and minimal intensity to be exceeded for a gene to be used. Default - 2 |
a filtered matrix
Implement three separate filtering functions: 1) Signal filtering, removing genes with expression at or below defined level, at or more defined proportion; 2) Absolute value of change, max-min difference should be larger than a defied threshold; 3) Variance filtering, variance should be larger than a defined threshold
Example from "Statistics and Data Analysis for Microarrays Using R and Bioconductor" book by Sorin Drăghici, p/ 778
Filtering should be done with caution, 10.1186/1471-2105-11-450.
## Not run: set.seed(2) mtx <- rbind(matrix(rnorm(200, mean = 9, sd = 2), ncol = 20), matrix(rnorm(200, mean = 10, sd = 5), ncol = 20)) dim(mtx) dim(gene_filter(mtx)) ## End(Not run)
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