HPAstainR: HPAStainR

In HPAStainR: Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

Description

Uses a protein/gene list to query Human Protein Atlas (HPA) staining data.

Usage

HPAStainR(
  gene_list,
  hpa_dat,
  cancer_dat = data.frame(),
  cancer_analysis = c("normal", "cancer", "both"),
  tissue_level = TRUE,
  stringency = c("normal", "high", "low"),
  scale_abundance = TRUE,
  round_to = 2,
  csv_names = TRUE,
  stained_gene_data = TRUE,
  tested_protein_column = TRUE,
  percent_or_count = c("percent", "count", "both"),
  drop_na_row = FALSE,
  adjusted_pvals = TRUE
)

Arguments

gene_list	A list of proteins or genes that you want to query the HPA staining data with.
hpa_dat	The data frame of normal HPA staining data data, required to run HPAStainR.
cancer_dat	The data frame of pathologic HPA staining data, required to run HPAStainr.
cancer_analysis	A character string indicating inclusion of cancer data in the result, must be one of 'normal' (default), 'cancer', or 'both'.
tissue_level	A boolean that determines whether tissue level data for the cell types are included. Default is TRUE
stringency	A character string indicating how stringent the confidence level of the staining findings have to be. Must be 'normal' (default), 'high', or 'low'.
scale_abundance	A boolean that determines whether you scale Staining Score based on the size of the gene list. Default is TRUE.
round_to	A numeric that determines how many decimals in numeric outputs are desired. Default 2.
csv_names	A Boolean determining if you want names suited for a csv file/pipeline, or for presentation. Default is TRUE giving csv names.
stained_gene_data	A boolean determining if there is a list of which proteins stained, TRUE is default.
tested_protein_column	A boolean determining if there is a column listing which proteins were tested, TRUE is default.
percent_or_count	A character string determining if percent of proteins stained, count of proteins stained, or both are shown for high, medium, and low staining. Must be 'percent' (default), 'count', or 'both'.
drop_na_row	A boolean that determines if cell types with no proteins tested are kept or dropped, default is FALSE.
adjusted_pvals	A boolean indicating if you want the p-values corrected for multiple testing. Default is TRUE.

Value

A tibble containing the results of HPAStainR.

Details

Calculation of the staining score below:

(\frac{h \times 100}{t}) + (\frac{m \times 50}{t}) + (\frac{l \times 25}{t})

Examples

   ## Below will give you the results found on the shiny app website
   ## This example also uses HPA_data_downloader output as an example
   HPA_data <- HPA_data_downloader(tissue_type = 'both', save_file = FALSE)
   HPA_out <- HPAStainR(c('PRSS1', 'PNLIP', 'CELA3A', 'PRL'),
   HPA_data$hpa_dat,
   HPA_data$cancer_dat,
   'both')

HPAStainR documentation built on Feb. 11, 2021, 2:01 a.m.