data-raw/depmap_22q1_TPM.R

In j-andrews7/CRISPRball: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

library(depmap)

gene <- "CDK2"
df <- depmap::depmap_TPM()
df$gene <- NULL
df$cell_line <- NULL

depmap.meta <- depmap::depmap_metadata()

df <- df[df$gene_name == gene, ]

df$cell_line_name <- depmap.meta$cell_line_name[match(df$depmap_id, depmap.meta$depmap_id)]
df$primary_disease <- depmap.meta$primary_disease[match(df$depmap_id, depmap.meta$depmap_id)]
df$lineage <- depmap.meta$lineage[match(df$depmap_id, depmap.meta$depmap_id)]
df$lineage_subtype <- depmap.meta$lineage_subtype[match(df$depmap_id, depmap.meta$depmap_id)]

df$hover.string <- paste0(
    "</br><b>Cell Line:</b> ", df$cell_line_name,
    "</br><b>log2(TPM+1):</b> ", format(round(df[["rna_expression"]], 3), nsmall = 3),
    "</br><b>Lineage:</b> ", df$lineage,
    "</br><b>Disease:</b> ", df$primary_disease
)

depmap_22q1_TPM <- df

write_csv(depmap_22q1_TPM, "data-raw/depmap_22q1_TPM.csv")

usethis::use_data(depmap_22q1_TPM, overwrite = TRUE)