In CharlesJB/FantomEnhancers.mm9: Position and normalized expression of Fantom's enhancers

Position and normalized expression of Fantom's enhancers

Charles Joly Beauparlant

This package and the underlying metagene code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

Installation

require(devtools)
devtools::install_github("CharlesJB/FantomEnhancers.hg19")

Loading the library

library("FantomEnhancers.hg19")

Main functions

get_fantom_enhancers

The get_fantom_enhancers functions returns a GRanges object with all the enhancers and no metadata columns:

get_fantom_enhancers()

get_fantom_enhancers_tpm

The get_fantom_enhancers_tpm returns a GRanges object with all the enhancers and selected metadata columns:

To get the expression of enhancers in A549:

get_fantom_enhancers_tpm(cell_lines = "A549")

To get the expression of enhancers in A549 and K562:

get_fantom_enhancers_tpm(cell_lines = c("A549", "K562"))

To merge all the columns for a cell line by calculating the mean value for each enhancers:

get_fantom_enhancers_tpm(cell_lines = c("A549", "K562"), merge.FUN = mean)

To merge all the columns for a cell line by calculating the sum for each enhancers:

get_fantom_enhancers_tpm(cell_lines = c("A549", "K562"), merge.FUN = sum)

It's also possible to create our own function, as long as it take a vector of numeric as input and outputs a single numeric value:

# We create a dummy function that returns first element of a vector
dummy_function <- function(x) {
  x[1]
}
get_fantom_enhancers_tpm(cell_lines = c("A549", "K562"), merge.FUN = dummy_function)

CharlesJB/FantomEnhancers.mm9 documentation built on May 6, 2019, 9:57 a.m.