get_fantom_tss_tpm: Get a GRanges object with the TPM values for specific cell...
In CharlesJB/FantomTSS.hg19: Position and normalized expression of Fantom's TSS

Description Usage Arguments Value See Also Examples

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

1	get_fantom_tss_tpm(cell_lines = NULL, merge.FUN = NULL)

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 (1827 columns).

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

A GRanges object with the metadata columns containing the expression value in TMP for the requested cell line(s), all 1827 experiments expression values are returned if cell_line is NULL. If the cell line(s) is not found, an empty GRanges is returned.

get_fantom_tss

get_fantom_library_name

# To get the TPM in A549 cell lines
  get_fantom_tss_tpm(cell_lines = "A549")

  # To get the TPM in A549 and in K562 cell lines
  get_fantom_tss_tpm(cell_lines = c("A549", "K562"))

  # To get the TPM K562 cell lines and merge metadata columns by returning
  # their mean value
  get_fantom_tss_tpm(cell_lines = "K562", merge.FUN = mean)