Connectivity Map in the context of Immune Response

Code for analysis of immunomodulator genes in the Connectivity Map dataset

For a tutorial, please refer to the file cp_analysis_TNBC_cells.Rmd.

The code is developed entirely in R using the R Studio development environment. In addition, the following packages are used:

• cmapR
• dplyr
• data.table
• ggplot2
• ggrepel
• pheatmap
• plyr
• skimr

The cmapR package is not available in CRAN as for this moment. To install the development version from GitHub: devtools::install_github("cmap/cmapR")

Data

All the data used for this project is available for download at GSE92742. The files needed in this project are:

GSE92742_Broad_LINCS_sig_info.txt

GSE92742_Broad_LINCS_sig_metrics.txt.gz

GSE92742_Broad_LINCS_cell_info.txt

GSE92742_Broad_LINCS_gene_info.txt.gz

GSE92742_Broad_LINCS_gene_info_delta_landmark.txt.gz

GSE92742_Broad_LINCS_pert_info.txt

GSE92742_Broad_LINCS_pert_metrics.txt.gz

GSE92742_Broad_LINCS_inst_info.txt.gz

GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx

The load_data.R file takes care of loading the data. Users need to set the path to the downloaded data by setting the variable CMAP_HOME to the desired location.

For example, in unix bash shell, this can be set by running: export CMAP_HOME=path/to/files

In a R Session, this can be set with the command Sys.setenv(CMAP_HOME="path/to/files")