Description Usage Arguments Value Examples
Takes an table corresponding to the contents of the snp_info.txt file from midas_merge.py and adds a column indicating whether the variant is synonymous or non-synonymous
1 | determine_snp_effect(info, nucleotides = c(A = 1, C = 2, G = 3, T = 4))
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info |
A data table corresponding to the contents of the snp_info.txt file produced by midas_merge. It must have columns: 'site_id', 'major_allele', 'minor_allele' and 'amino_acids'. The aminoacid column must contain a string of four comma-separated values indicating the aminoacid encoded for each variant (eg. 'V,L,V,L'). |
nucleotides |
Named vector indicating the position of each nucleotide that corresponds to the amino_acids column in info. The default corresponds to MIDAS v1.3.1 default. |
The same data table passed as info with a factor column 'snp_effect' added.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | library(HMVAR)
# Get file paths
midas_dir <- system.file("toy_example/merged.snps/", package = "HMVAR")
map <- readr::read_tsv(system.file("toy_example/map.txt", package = "HMVAR"),
col_types = readr::cols(.default = readr::col_character())) %>%
dplyr::select(sample = ID, Group)
# Read data
midas_data <- read_midas_data(midas_dir = midas_dir, map = map, cds_only = TRUE)
info <- determine_snp_effect(midas_data$info) %>%
determine_snp_dist(freq = midas_data$freq,
depth = midas_data$depth, map = map,
depth_thres = 1, freq_thres = 0.5)
info
mktable <- info %>%
split(.$gene_id) %>%
purrr::map_dfr(mkvalues,
.id = "gene_id")
mktable
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