R/variationFilter.R
VERBOSE.Rd
subset an expression dataset by extracting genes based on their level of variation
VERBOSE(v, ...)
dat | an expressionSet object |
---|---|
score | type of variation measure to use (can be 'mad', 'sd', or 'cv') |
dir | direction of the gene ranking ('top': highest varying genes; 'bottom': lowest varying genes) |
transform | transform the data before measuring variation |
ngenes | number of top (or bottom) genes to extract |
do.plot | plot the center vs. scale plot with selected genes highlighted |
do.log | indicates whether to log the "x", "y", or "xy" axes, or "" none |
the filtered expressionSet object
# select the top 100 genes by median absolute deviation (mad) and also generate plot # Use example data, for data set information: ?eSet.brca.100 data(eSet.brca.100)#> Warning: data set ‘eSet.brca.100’ not foundvariationFilter(eSet.brca.100,score='mad',ngenes=50,do.plot=TRUE)#> Error in nrow(dat): object 'eSet.brca.100' not found