get_fantom_enhancers_counts: Get a GRanges object with the counts values for specific cell...

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

Description

Returns a GRanges with metadata columns corresponding to the requested cell type enhancer expression (in counts).

Usage

get_fantom_enhancers_counts(cell_lines = NULL, merge.FUN = NULL)

Arguments

cell_lines

The cell line(s) to fetch. Must be a vector of character. The function will look for the pattern (with grepl) to find case-insensitive match(es) with this param in the Fantom's experiments sample names. If NULL, this will return a GRanges object with all the Fantom's experiments. The metadata columns will be named using the cell_type param. When merge.FUN is NULL and there is multiple experiment for the same cell line, a counter will be added after each name to ensure all metadata colnames are unique (i.e.: A549_1, A549_2, A549_3). If NULL, the experiment names will be used for each metadata colnames. Default: NULL.

merge.FUN

A function to merge the TPM when there is more than one column for the same cell type. Must take a vector of numeric as input and returns a single numeric value. Default: NULL

Value

A GRanges object with the metadata columns containing the expression value in counts for the requested cell line(s), all experiments expression values are returned if cell_line is NULL. If the cell line(s) is not found, an empty GRanges is returned.

See Also

get_fantom_enhancers

get_fantom_enhancers_tpm

get_fantom_fantom_library_name

Examples

# To get the counts in lung
  get_fantom_enhancers_counts(cell_lines = "lung")

  # To get the counts in lung and heart
  get_fantom_enhancers_counts(cell_lines = c("lung", "heart"))

  # To get the counts lung and merge metadata columns by returning
  # their mean value
  get_fantom_enhancers_counts(cell_lines = "lung", merge.FUN = mean)

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