README.md

In CharlesJB/FantomTSS.hg19: Position and normalized expression of Fantom's TSS

FantomTSS.hg19

The goal of this package is to easily extract the genomic positions and the normalized expression of Fantom's TSS (in TPM) in hg19.

Installation

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

Main functions

The get_fantom_tss functions returns a GRanges object with all the tss and no metadata columns:

get_fantom_tss()

The get_fantom_tss_tpm returns a GRanges object with all the tss and selected metadata columns:

# To get the expression of tss in A549
get_fantom_tss_tpm(cell_lines = "A549")

# To get the expression of tss in A549 and K562
get_fantom_tss_tpm(cell_lines = c("A549", "K562"))

# To merge all the columns for a cell line by calculating the mean value for
# each tss
get_fantom_tss_tpm(cell_lines = c("A549", "K562"), merge.FUN = mean)

# To merge all the columns for a cell line by calculating the sum for each
# tss
get_fantom_tss_tpm(cell_lines = c("A549", "K562"), merge.FUN = sum)

Reproduce the datasets

If you wish to reproduce the datasets, you can use the prepare_datasets function. From a R session in the packages main directory:

library(devtools)
library(data.table)
load_all()
source("data-raw/data.R")
prepare_datasets()

Note that this will download large files (~800 MB) from Fantom's web page. You will also need to reinstall the package if you want to use those new datasets.

CharlesJB/FantomTSS.hg19 documentation built on May 6, 2019, 9:57 a.m.