removed text about downloading pre-calculated probs file

vignettes/recla-analysis.Rmd

@@ -35,29 +35,22 @@ gm <- pseudomap$`8`
 ```
 
 
-Typically, we would use the hidden Markov model from Broman (2012) to calculate 36-state genotype probabilities for autosomal markers. We would use the following line of code to do that.
+We use the hidden Markov model from Broman (2012) to calculate 36-state genotype probabilities for autosomal markers. We use the following line of code to do that.
 
 ```{r calc-genoprobs-code, eval = FALSE}
 probs <- calc_genoprob(recla, map = pseudomap, cores = 1)
 ```
 
-We would then convert the genotype probabilities to haplotype dosages.
+We then convert the genotype probabilities to haplotype dosages.
 
 ```{r calc-aprobs, eval = FALSE}
 aprobs <- genoprob_to_alleleprob(probs)
 ```
 
-However, to save computing time when creating vignettes, we instead read pre-calculated 8-state founder allele dosages from Zenodo.
-
-```{r}
+```{r, echo = FALSE}
 url <- "https://zenodo.org/record/2652931/files/recla-aprobs.rds?download=1"
 dir.create("tmp") #create a directory that we'll delete later
 download.file(url, destfile = "tmp/recla-aprobs.rds")
-```
-
-After downloading the rds file, we read it into our R session.
-
-```{r}
 aprobs <- readRDS("tmp/recla-aprobs.rds")
 unlink("tmp", recursive = TRUE) # delete the tmp directory
 ```