load_iPAS: Load integrative Pathway Activity Signatures (iPAS)

In uc-bd2k/iPAS: integrative Pathway Activity Signatures (iPAS)

Load integrative Pathway Activity Signatures (iPAS)

Description

Load integrative Pathway Activity Signatures (iPAS)

Usage

load_iPAS(
  method = c("ensemble", "cl", "mtl", "legacy_cl"),
  cell_line = c("A375", "A549", "HA1E", "HCC515", "HEKTE", "HEPG2", "HT29", "MCF7",
    "NPC", "PC3", "SW480", "VCAP"),
  genes = c("entrez", "symbol")
)

Arguments

method	The method used to create the iPAS signatures: "ensemble" refers to consensus signatures combined with weights determined by ensemble learning, "cl" refers to signatures created using data from one cell line only, "mtl" refers to "multi-task learning" signatures, "legacy_cl" refers to the version of signatures (from one cell line) published in Ren et al. 2020 (slightly different method than recent signatures).
cell_line	LINCS cell line to load signatures from (if applicable)
genes	format of rownames for genes (entrez ids or gene symbols)

Value

a list object containing the requested Pathway Activation Signatures (iPAS)

uc-bd2k/iPAS documentation built on May 27, 2022, 10:13 p.m.