PrepareReference: Prepare Drug Reference.

In lanagarmire/Asgard: A Single-cell Guided pipeline for Accurate Repurposing of Drugs

Prepare Drug Reference.

Description

Prepare tissue specific drug reference Profiles from L1000 drug response data.

Usage

PrepareReference(
  cell.info = NULL,
  gene.info = NULL,
  GSE70138.sig.info = NULL,
  GSE92742.sig.info = NULL,
  GSE70138.gctx = NULL,
  GSE92742.gctx = NULL,
  Output.Dir = "./"
)

Arguments

cell.info	The local path and the name of the cell.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70138/suppl/GSE70138_Broad_LINCS_cell_info_2017-04-28.txt.gz .
gene.info	The local path and the name of the gene.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70138/suppl/GSE70138_Broad_LINCS_gene_info_2017-03-06.txt.gz .
GSE70138.sig.info	The local path and the name of the cell.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70138/suppl/GSE70138_Broad_LINCS_sig_info_2017-03-06.txt.gz .
GSE92742.sig.info	The local path and the name of the cell.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92742/suppl/GSE92742_Broad_LINCS_sig_info.txt.gz .
GSE70138.gctx	The local path and the name of the cell.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70138/suppl/GSE70138_Broad_LINCS_Level5_COMPZ_n118050x12328_2017-03-06.gctx.gz .
GSE92742.gctx	The local path and the name of the cell.info text file. It's downloaded from https://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92742/suppl/GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx.gz .
Output.Dir	The output directory for the generated files.

Details

This function converts L1000 data to the tissue specific drug rank matrix.

lanagarmire/Asgard documentation built on Jan. 25, 2024, 3:28 p.m.