Subsetting SNP Dataset by Sample ID
Sunaina Nayak
2025-01-09
Setup
snp_data_path <- params$snp_dataset
sample_id <- params$sample_idlibrary("dplyr")
library("ggplot2")
library("knitr")
library("devtools")
source("code/functions/rscript.R")Project Description
Multiple different samples of the SARS-CoV2 virus were taken and then
genotyped. After being genotyped, they were compared to reference
genome. A single nucleotide polymorphism, or SNP,is anywhere where the
samples has a different nucleotide than the reference genome at a given
loci. Base R and dyplr Wickham
et al. (2023) were used to subset the data by sample id.
Base R and ggplot2 Wickham
(2016) were used to create figures from the subsetted data.
Rstudio, dyplr, and ggplot2 has
allowed us to isolate and visualize SNP variants by sample ID.
Subsetting Data
# return function
result <- subset_snp_data(snp_data_path, sample_id)write.csv(result, paste0("output/snp_subset_", sample_id, ".csv"))Figures
# use ggplot to make a scatterplot colored by sample
result %>%
ggplot(aes(x = pos,
y = qual,
color = sample)) +
geom_point() +
labs(title = "SNP Quality by Position in the SARS-CoV2 Genome")
ggsave(paste0("output/figures", sample_id, "snp_quality_by_position.png"))# use ggplot to make a scatterplot colored by sample
result %>%
ggplot(aes(x = alt,
y = pos,
color = sample)) +
geom_point() +
labs(title = "Change from reference by Position in the SARS-CoV2 genome")
ggsave(paste0("output/figures", sample_id, "nucleotide_change_by_position.png"))Session Info
session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.4.1 (2024-06-14 ucrt)
## os Windows 11 x64 (build 22631)
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.utf8
## ctype English_United States.utf8
## tz America/Los_Angeles
## date 2025-01-09
## pandoc 3.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
##
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##
## ──────────────────────────────────────────────────────────────────────────────Sources Cited
Wickham,H. et al. (2023) Dplyr: A grammar of data
manipulation.
Wickham,H. (2016) ggplot2:
Elegant graphics for data analysis Springer-Verlag New York.