README.md

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

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)

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