index.Rmd

---
title: "modeling_result"
author: "Crystal Shan"
date: "2024-02-06"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r packages, include=FALSE}
library(tidyverse)
library(DT)
```

# Feature-Selected Model: Phenotype Rank-Normalized CPM
```{r include=FALSE, warning=FALSE}
# read in feature selected rank-normalized CPM model
fs_rank_norm_cpm <- data.table::fread("website/data/modeling_results/modelingResults_featureSelectedRankNormCPM_QTLs_1E-5PvalCutoff_3cts.txt")

fs_rank_norm_cpm$reQTL_pval <- as.numeric(fs_rank_norm_cpm$reQTL_pval)
fs_rank_norm_cpm$reQTL_beta <- as.numeric(fs_rank_norm_cpm$reQTL_beta)
fs_rank_norm_cpm$PBSeQTL_pval <- as.numeric(fs_rank_norm_cpm$PBSeQTL_pval)
fs_rank_norm_cpm$PBSeQTL_beta <- as.numeric(fs_rank_norm_cpm$PBSeQTL_beta)
fs_rank_norm_cpm$IFNeQTL_pval <- as.numeric(fs_rank_norm_cpm$IFNeQTL_pval)
fs_rank_norm_cpm$IFNeQTL_beta <- as.numeric(fs_rank_norm_cpm$IFNeQTL_beta)

#sum(!is.na(fs_rank_norm_cpm$reQTL_pval) & !is.numeric(fs_rank_norm_cpm$reQTL_pval))
```


```{r echo=FALSE, warning=FALSE, message=FALSE}
# init. URL base
url_gene_base <- "https://www.genecards.org/cgi-bin/carddisp.pl?gene="
url_snp_base <- "https://www.ncbi.nlm.nih.gov/snp/"

# embed hyperlinks for each SNP and gene
fs_rank_norm_cpm <- fs_rank_norm_cpm %>%
  mutate(
    gene = str_c("<a href=", url_gene_base, GENE, " target=_blank", ">", GENE, "</a>"),
    snp = str_c("<a href=", url_snp_base, SNP, " target=_blank", ">", SNP, "</a>"),
    plots = str_c("<a href=website/plots/", GENE, "_", SNP, "_", "pairedPlot_3donorColored_CPM.png target=_blank>Paired Plot CPM</a>"),
    Actions = str_c("<a href=","https://www.gtexportal.org/home/browseEqtls?location=",GENE, " target=_blank", ">", "IGV Browser", "</a>")) %>%
  select(pair, snp, gene, plots, Actions, everything(), -c(GENE, SNP))

df_html <- fs_rank_norm_cpm %>%
  datatable(escape = F, style = "auto")
df_html
```