tests/testthat/test-rsid2varinfo.R

In letaylor/bioutils: Useful functions for computational biology

context('rsid2varinfo')

df_test1_order <- c('rs8050136', 'rs780094', 'rs1694', 'rs66698963')
df_test1 <- data.frame(
    'rs_id' = c('rs8050136', 'rs780094', 'rs1694', 'rs66698963'),
    'chr_name' = c(16, 2, 18, 11),
    'chrom_start' = c(53816275, 27741237, 25398056, 61602537),
    'ref_allele' = c('C', 'T', 'A', 'ACTTCTCCCTGCCTCCCCAGGG'),
    'alt_allele' = c('A', 'C', 'T', '-'),
    stringsAsFactors = FALSE
)
row.names(df_test1) <- df_test1$rs_id


test_that('rsid2varinfo returns correct data.frame', {
    expect_equal(
        rsid2varinfo(c(df_test1_order, 'rs66698963'))[df_test1_order,],
        df_test1
    )
})