Take a sample of rows from non-significant results

May be useful when plotting Manhattan or Q-Q plots for GWAS results to speed up plotting.

Usage

sample_nonsig_results(df, pval_col = "P", sig = 5e-08, n, prop)

Arguments

df

A data frame.

pval_col

Name of column in df containing p values.

sig

Significance threshold. P values equal to or greater than this will be sampled.

n, prop

Provide either n, the number of rows, or prop, the proportion of rows to select. If neither are supplied, n = 1 will be used.

If a negative value of n or prop is provided, the specified number or proportion of rows will be removed.

If n is greater than the number of rows in the group (or prop > 1), the result will be silently truncated to the group size. If the proportion of a group size does not yield an integer number of rows, the absolute value of prop*nrow(.data) is rounded down.

Value

A data frame.

Examples

dummy_manhattan_df() %>%
  sample_nonsig_results(pval_col = "P",
                        sig = 0.001,
                        n = 2)
#> # A tibble: 6 × 5
#>   CHR   SNP    BETA    SE           P
#>   <chr> <chr> <dbl> <dbl>       <dbl>
#> 1 1     b       0    0.02 0.0001     
#> 2 1     c      -0.1  0.03 0.000000001
#> 3 11    l      -0.1  0.03 0.0001     
#> 4 11    o      -0.1  0.03 0.0001     
#> 5 2     d       0.1  0.01 0.01       
#> 6 3     h       0    0.02 0.05