fantom_to_expset: GAPGOM - fantom_to_expset()

In Berghopper/GAPGOM: GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Description

Convert raw data.table/data.frame fantom5 object to a proper ExpressionSet.

Usage

fantom_to_expset(fanraw, species, filter = TRUE, verbose = FALSE)

Arguments

fanraw	raw data.table object from the fantom_load_raw() function.
species	either "human" or "mouse". This is important because both datasets have different metadata/stats
filter	Filter, this causes only entries to be added that have an entrez ID. Normally this should be left on default (TRUE) because all algorithms in this library need the entrez IDs for translation.
verbose	Switch to TRUE for extra messages. Default=FALSE

Details

This function converts fantom5 data and converts it into an ExpresionSet. This ExpressionSet is then returned. This function only accepts the RLE normalized data!

Value

The resulting ExpressionSet contains the original data. The expressiondata can be found under assayData(ExpressionSet)[["exprs"]] Other information (first 6 info columns) can be found under; pData(featureData(ExpressionSet))

Examples

fantom_file <- fantom_download(organism = "mouse", noprompt = TRUE)
ft5 <- fantom_load_raw(fantom_file, verbose = TRUE, example = TRUE)
expset <- fantom_to_expset(ft5, "mouse", verbose = TRUE)

Berghopper/GAPGOM documentation built on July 2, 2020, 11:57 p.m.