Applies a number of filters on a spliceR object to reduce data set size before running downstream analyses.
preSpliceRFilter(spliceRobject, filters, expressionCutoff=0)
vector, giving the filters that should be applied - any combinations of 'geneOK', 'expressedGenes', 'sigGenes', 'isoOK', 'expressedIso', 'isoClass' and/or 'sigIso'. Works only for data from cufflinks, as a manually generated
Numeric, giving the expression threshold (often in FPKM) used for the 'expressedGenes' and 'expressedIso' filter. Default value is 0.
Often, many genes and isoforms are flagged as not "OK" or "LOWDATA" by Cufflinks, indicating low confidence in these. This function is handy for reducing the data size of a Cufflinks data set to reduce running times for downstream analyses.
preSpliceRFilter removes trancsripts from the dataset permanently, reducing size, while the filter options of
annotatePTC only selects transcripts for analysis, but does not remove any data.
SpliceRList with transcripts after filtering.
Kristoffer Vitting-Seerup, Johannes Waage
Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.
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