Filters markers or genes/transcripts based on a threshold applied to their GWAS or DE score, and log2(fold-change) (if applicable). For a set of candidate genes, simply returns the list. Note that markers or genes with a missing score or log2(fold-change) will be removed from the dataset.
Usage
apply_threshold(x, score_thr = 0, log2fc_thr = 0)
# S3 method for class 'GWAS_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)
# S3 method for class 'DE_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)
# S3 method for class 'CAN_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)
# S3 method for class 'CUSTOM_data'
apply_threshold(x, score_thr = 0, log2fc_thr = 0)
# Default S3 method
apply_threshold(x, score_thr = 0, log2fc_thr = 0)Arguments
- x
Either a
GWAS_data,DE_data,CAN_dataorCUSTOM_dataobject.- score_thr
Numeric, threshold to use on markers' or genes/transcripts' score. Only markers or genes with a score equal to or higher than this threshold will be retained. Default value is 0. Ignored for
CAN_data.- log2fc_thr
Numeric, threshold to use on the absolute value of genes/ transcripts' log2(fold-change). Only genes/transcripts with an absolute log2(fold-change) equal to or higher than this threshold will be retained. Ignored for
GWAS_data,CAN_dataandCUSTOM_data.
Examples
x <- get_example_data()
## For GWAS results
apply_threshold(GWAS_data(x[["GWAS"]]), score_thr = 4)
#> # A tibble: 37 × 4
#> id chromosome position score
#> <chr> <chr> <dbl> <dbl>
#> 1 ST4.03ch00_22680252 ST4.03ch00 22680252 4.41
#> 2 ST4.03ch01_6317643 ST4.03ch01 6317643 4.15
#> 3 ST4.03ch01_7671100 ST4.03ch01 7671100 4.43
#> 4 ST4.03ch01_8653747 ST4.03ch01 8653747 4.69
#> 5 ST4.03ch01_12842648 ST4.03ch01 12842648 6.85
#> 6 ST4.03ch01_13334335 ST4.03ch01 13334335 5.24
#> 7 ST4.03ch01_13544786 ST4.03ch01 13544786 4.00
#> 8 ST4.03ch01_42743974 ST4.03ch01 42743974 4.00
#> 9 ST4.03ch01_42949112 ST4.03ch01 42949112 4.18
#> 10 ST4.03ch01_52529264 ST4.03ch01 52529264 4.85
#> # ℹ 27 more rows
## For DE results - in second line, no threshold is applied
## on the log2(fold-change)
apply_threshold(DE_data(x[["DE"]]), score_thr = -log10(0.05), log2fc_thr = 1)
#> # A tibble: 5 × 9
#> gene chromosome padj log2FoldChange start end label score position
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 PGSC0003D… ST4.03ch01 0.0488 1.61 8.15e7 8.15e7 Gene… 1.31 8.15e7
#> 2 PGSC0003D… ST4.03ch03 0.0488 1.14 3.49e7 3.49e7 Gene… 1.31 3.49e7
#> 3 PGSC0003D… ST4.03ch03 0.0184 3.06 5.99e7 5.99e7 Phos… 1.73 5.99e7
#> 4 PGSC0003D… ST4.03ch05 0.0414 1.10 3.47e6 3.47e6 Cons… 1.38 3.47e6
#> 5 PGSC0003D… ST4.03ch09 0.0328 1.51 5.40e7 5.40e7 Vici… 1.48 5.40e7
apply_threshold(DE_data(x[["DE"]]), score_thr = -log10(0.05), log2fc_thr = 0)
#> # A tibble: 57 × 9
#> gene chromosome padj log2FoldChange start end label score position
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 PGSC000… ST4.03ch00 0.0488 0.838 3.80e7 3.80e7 Pept… 1.31 3.80e7
#> 2 PGSC000… ST4.03ch01 0.0362 -0.181 5.83e7 5.83e7 Cons… 1.44 5.83e7
#> 3 PGSC000… ST4.03ch01 0.0488 1.61 8.15e7 8.15e7 Gene… 1.31 8.15e7
#> 4 PGSC000… ST4.03ch01 0.00465 0.438 8.45e7 8.45e7 Phi-2 2.33 8.45e7
#> 5 PGSC000… ST4.03ch02 0.0488 0.325 2.26e7 2.26e7 Cons… 1.31 2.26e7
#> 6 PGSC000… ST4.03ch02 0.0266 0.768 3.32e7 3.32e7 Leuc… 1.58 3.32e7
#> 7 PGSC000… ST4.03ch02 0.0488 0.381 4.14e7 4.14e7 Cons… 1.31 4.14e7
#> 8 PGSC000… ST4.03ch02 0.0314 0.663 4.23e7 4.23e7 Home… 1.50 4.23e7
#> 9 PGSC000… ST4.03ch03 0.0488 -0.804 5.33e5 5.41e5 SNF2… 1.31 5.37e5
#> 10 PGSC000… ST4.03ch03 0.0493 -0.345 9.26e6 9.26e6 Dihy… 1.31 9.26e6
#> # ℹ 47 more rows
## No effect on the Candidate genes
apply_threshold(CAN_data(x[["CAN"]]))
#> # A tibble: 32 × 7
#> id chromosome start end name gene_name position
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <dbl>
#> 1 PGSC0003DMG400003155 ST4.03ch03 46757152 46762127 4CL 4-coumar… 4.68e7
#> 2 PGSC0003DMG400014223 ST4.03ch03 57466692 57469946 4CL2 4-coumar… 5.75e7
#> 3 PGSC0003DMG400011189 ST4.03ch07 1001854 1006278 HQT HQT 1.00e6
#> 4 PGSC0003DMG400005492 ST4.03ch05 36342746 36347409 PAL phenylal… 3.63e7
#> 5 PGSC0003DMG400005279 ST4.03ch05 42523943 42525912 peroxi… peroxida… 4.25e7
#> 6 PGSC0003DMG400007782 ST4.03ch03 38537202 38540209 PHO1A PHO1A 3.85e7
#> 7 PGSC0003DMG400023182 ST4.03ch02 10091564 10093164 LIPIII… LipIII27 1.01e7
#> 8 PGSC0003DMG400029576 ST4.03ch08 45676042 45677832 PPOs Polyphen… 4.57e7
#> 9 PGSC0003DMG400018924 ST4.03ch08 45778567 45780333 NA Polyphen… 4.58e7
#> 10 PGSC0003DMG400018919 ST4.03ch08 45793661 45794229 NA Polyphen… 4.58e7
#> # ℹ 22 more rows