Given two tsv tables, one including ligand-receptor pairs, and the other including receptor-target pairs, and a data set, inner-join the two tables and make sure no ligands, receptors, or targets are missing from the data. This function returns a summary table of all requested markers. If the data is a subset of some larger study, genes may be reported (a column exists in the data matrix) for which zero copies were observed. In this case, "dropout in subset" applies. There are also known gene symbols which were not measured in the study (no corresponding row exists in the data matrix). In this case, "missing from all subsets" applies.

ImportPathway(
  lig_table = NULL,
  rec_table = NULL,
  lig_table_path,
  rec_table_path = NULL,
  data,
  gene_names = NULL
)

Arguments

lig_table

a data frame with "ligand" in column 1 and "receptor" in column 2

rec_table

a data frame with "receptor" in column 1, "target" in column 2, and up/down "direction"

lig_table_path

a tsv/csv file with "ligand" in column 1 and "receptor" in column 2

rec_table_path

a tsv/csv file with "receptor" in column 1, "target" in column 2, and up/down "direction" in column 3

data

a matrix of the data, with gene names as row names (required if no gene list provided)

gene_names

an optional list of gene names (required if rownames of data are null)

Value

a list containing:

lignames

vector of all ligands

recnames

vector of all receptors

targets

vector of all targets

pathway

a table with combined pathway information

pathway_removed

a table with markers excluded

removed

a table with the excluded markers