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Check if input is a GenomicRanges object, plus optional sanity check of column names

Source: R/swissArmyKnife.R
gr_sanitycheck.Rd

Simple check if the input is a GenomicRanges object, plus includes an additional functionality to perform a smart, transparent sanity check of expected column names.

Usage

gr_sanitycheck(query_gr, expected_cols = NULL)

Arguments

query_gr

Suspected GenomicRanges-like object to test

expected_cols

Vector of character strings to check for consistency in columns of query GenomicRanges, default: NULL

Value

TRUE or FALSE

Examples

# Not a GR
gr_sanitycheck(query_gr = braf_dnase_demo_dt_hg38)
#> [1] FALSE
# Just a GR
gr_sanitycheck(query_gr = kras_dnase_demo_gr_hg38)
#> [1] TRUE
# GR with correct columns
gr_sanitycheck(query_gr = kras_dnase_demo_gr_hg38,
               expected_cols = c("signalValue","pValue","biospecimen","gene"))
#> [1] TRUE
# GR with less columns than expected
gr_sanitycheck(query_gr = kras_dnase_demo_gr_hg38[,-3],
               expected_cols = c("signalValue","pValue","biospecimen","gene"))
#> # A tibble: 1 × 8
#>   seqnames    start      end strand width signalValue pValue gene 
#>   <chr>       <int>    <int> <chr>  <dbl>       <dbl>  <dbl> <chr>
#> 1 chr12    25241134 25241673 *        540        13.8   22.7 KRAS 
#> ✖ Input GenomicRanges object had less columns than expected - missing columns: biospecimen
#> [1] FALSE