data-raw/cell_info.R

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

## code to prepare `cell_info` dataset goes here

## Download and unzip the GSE92742_Broad_LINCS_cell_info.txt.gz file
## from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742
library(readr); library(dplyr); library(magrittr)
cell_info <- read_tsv("~/insync/project/lincs_gse92742_dataset_analysis/data/GSE92742_Broad_LINCS_cell_info.txt")
cell_name <- c("NEU", "A549", "PC3", "VCAP", "MCF7", "ASC", "SKB", "PHH", 
               "NPC", "HT29", "FIBRNPC", "HCC515", "A375", "HA1E", "CD34", "HL60", 
               "U937", "HEK293T", "HEPG2", "HUH7", "NOMO1", "THP1", "BT20", "HS578T", 
               "MCF10A", "MDAMB231", "SKBR3", "NKDBA", "JURKAT", "U266")
# 30 cell types tested in `lincs` database from the `signatureSearchData` package  
cell_info %<>% dplyr::filter(base_cell_id %in% cell_name & 
                !duplicated(paste(cell_info$base_cell_id, cell_info$sample_type, sep="_"))) %>%
    dplyr::select(c("cell_id","sample_type","primary_site","subtype", "donor_sex")) %>% 
    dplyr::rename("cell_type"="sample_type")
# replace "primary" as "normal" in sample_type column
cell_info %<>% mutate(cell_type=gsub("primary","normal",cell_type))
#write_tsv(cell_info, "~/insync/project/GESS_and_FEA/data/cell_info.tsv")
# replace -666 as unknown
cell_info[cell_info == "-666"] <- "unknown"
# manually update some info according to https://lincs.hms.harvard.edu/db/cells/
cell_info$primary_site[cell_info$cell_id=="NEU"] <- "nervous system"
cell_info$donor_sex[cell_info$cell_id=="MCF10A"] <- "F"

usethis::use_data(cell_info, overwrite=TRUE)