garyAnalysis.Rmd

---
title: "GaryAnalysis"
author: "Brian S. Yandell"
date: "12/19/2017"
output: html_document
---

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

```{r message=FALSE}
library(dplyr)
library(qtl2)
library(qtl2feather)
library(qtl2pattern)
library(stringr)
library(purrr)
```

```{r}
gary_anal <- system("grep '^# Phenotype' QTLmaps/Script.R", intern = TRUE) %>%
  str_replace("= ", "") %>%
  str_split("[:|,] +") %>%
  map(function(x) data.frame(t(x), stringsAsFactors = FALSE)) %>%
  bind_rows %>%
  rename(short = X2,
         transf = X4,
         covar = X6) %>%
  select(short, transf, covar)
```

Need to get translation of names. First modified Script.R to have one rename per line.


```{r}
renames <- system("sed -n -e '/^  rename/,/^names/{ /^names/d; p; }' QTLmaps/Script.R | sed 's/rename.//' | sed s/,$// | sed 's/ = /,/' | sed 's/ *//'", intern = TRUE)
renames <- str_split(renames, ",") %>%
  map(function(x) x[1:2]) %>%
  as.data.frame %>%
  t %>%
  as.data.frame(stringsAsFactors = FALSE)
 colnames(renames) <- c("short", "pheno")
 rownames(renames) <- NULL
 renames
```

```{r}
gary_anal$pheno <- gary_anal$short
m <- match(renames$short, gary_anal$short, nomatch = 0)
gary_anal$pheno[m] <- renames$pheno[m>0]
gary_anal
```

```{r}
(gary_anal <- gary_anal %>%
  mutate(covar = ifelse(covar %in% c("None","None."), "", covar),
         covar = str_replace(covar, " \\+ ", ",")) %>%
  mutate(transf = ifelse(transf == "sqrt transform", "sqrt", transf)))
```

Now need to add entries to `analyses_tbl` for additional covariates?
But I am not convinced that they actually work as desired.