LocusXcanR: LocusXcanR: An R Shiny App to Visualize TWAS Results...

In amanda-tapia/LocusXcanR: What The Package Does (one line, title case required)

Description

LocusXcanR allows users to import TWAS and GWAS results (and additional important details) in order to visualize them together in a single web page application via R Shiny and facilitates TWAS results interpretation in context.

Usage

LocusXcanR(
  twas_result,
  pvalthresh,
  weight_tbl,
  study_name = "",
  pred_exp_corr,
  conditional_present = FALSE,
  multiple_tissues = FALSE,
  known_variants,
  known_gwas,
  db_genes,
  all_gwas,
  ld_gwas,
  ref_expr_name = "",
  head_details = "",
  method_details = "",
  primary_tissue,
  meta_present = FALSE,
  meta_thresh,
  ideogram_present = FALSE,
  genome_build,
  cytoband_ds,
  add_UI = "",
  add_Server = ""
)

Arguments

twas_result	character, file path to TWAS results (required). See Details for required column names.
pvalthresh	numeric, -log10 p-value threshold for TWAS results (required).
weight_tbl	character, file path to TWAS weights database (required). See Details for required column names.
study_name	character, the name of the study (optional, default is missing)
pred_exp_corr	character, file path to predicted expression correlation (required). See Details for required column names.
conditional_present	logical, TRUE if conditional analysis results are available for plotting, FALSE otherwise (default is FALSE)
multiple_tissues	logical, TRUE if TWAS results are available from more than one tissue, FALSE if TWAS results are only available from a single tissue or a multi-tissue analysis (default is FALSE)
known_variants	character, file path to known GWAS variants (required). See Details for required column names.
known_gwas	character, file path to study GWAS data matching known variants (required)
db_genes	character, file path to a list of genes in the database (required)
all_gwas	character, file path to study GWAS data (required)
ld_gwas	character, file path to the LD among study variants or an LD reference panel (required)
ref_expr_name	character, name of the reference expression data set used in the analysis (optional, default is missing)
head_details	character, any additional header details to be included in the app (optional, default is no details). HTML formatting commands may be used.
method_details	character, detailed methods section (optional, default is no details). HTLM formatting commands may be used.
primary_tissue	character, if multiple tissues are available for analysis, list the name of the primary tissue (required if multiple_tissues = TRUE)
meta_present	logical, TRUE if results from TWAS meta-analysis are present for comparison, FALSE otherwise (optional, default is FALSE)
meta_thresh	numeric, p-value threshold for meta-analysis results (required if meta_present=TRUE)
ideogram_present	logical, TRUE if an ideogramTrack should be plotted, FALSE otherwise (optional, default is FALSE)
genome_build	character, the genome build for the ideogramTrack data (required if ideogram_present = TRUE)
cytoband_ds	character, file path to the cytogenic bands data set (required if ideogram_present = TRUE)
add_UI	character, additional elements to add to UI (optional, default is missing)
add_server	character, additional elements to add to server (optional, default is missing)

Details

Please reference the vignette here () for further details on required and optional variables for each input dataset

Created by: Amanda L. Tapia, Date: June 8, 2020, Updated: December 16, 2020

Value

An R Shiny application

Examples

# This is an example with only the required parameters


# This is an example with all parameters

amanda-tapia/LocusXcanR documentation built on March 9, 2021, 7:36 p.m.