write_list_as_gmt: Saves to file list of element combinations and most central...

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Saves to file list of element combinations and most central element from each grouping

Description

Creates a file with one tab separated line per each cluster of elements formatted as central_element__clusterid, comment, full list of elements in this gene signature with NA's for extra spots to length of largest cluster

Usage

write_list_as_gmt(
  cluster_members,
  central_elements,
  output_path = file.path(getwd(), "output_file.gmt.txt"),
  empty_cell = "",
  display_output = F
)

Arguments

cluster_members	Named list of clusters ( names will be used as clusterid's )
central_elements	Named list of central elements ( i.e. features ) from each cluster ( same length as cluster_members with matching names )
output_path	One-length character vector with fully qualified path to output file
empty_cell	Filler for empty cells. Typically ” or NA. Note there is a gene called 'NA'. It's in the influenza genome but still...
display_output	Boolean option to display which elements are in the final signatures. For gene signatures this will typically be too much information to display

Value

Returns gene signature data as saved to file

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.