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

Position and normalized expression of Fantom's tss

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

TODO

Loading the library

library("FantomTSS.hg19")

Main functions

get_fantom_tss

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

get_fantom_tss()

get_fantom_tss_tpm

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)

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_tss_tpm(cell_lines = c("A549", "K562"), merge.FUN = dummy_function)

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