FantomEnhancers.mm9

The goal of this package is to easily extract the genomic positions and the normalized expression of Fantom's enhancers (in TPM) in mm9.

Installation

require(devtools)
devtools::install_github("CharlesJB/FantomEnhancers.mm9")

Main functions

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

get_fantom_enhancers()

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

# TODO: Change cell lines for murine cell lines
# 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)