This function retrieves a filtered genes table based on specified criteria.
get_filtered_genes_table(
GeneDiscoveRobject = NULL,
name = NULL,
pvalue = NULL,
oddsRatio = NULL,
sign = NULL
)A GeneDiscoveR object containing the filtered genes.
The name of the gene.
The p-value of the gene.
The odds ratio of the gene.
The sign of the gene.
A filtered genes table that matches the specified criteria.
# Create a GeneDiscoveR object
N0sDir <- system.file("extdata", "N0-1dot3-6", package = "GeneDiscoveR")
overallsDir <- system.file("extdata", "Comparatives-1dot3-6", package = "GeneDiscoveR")
dataFile <- system.file("extdata", "annotatedCDSs.tsv", package = "GeneDiscoveR")
minInflation <- 1.3
maxInflation <- 6
stepInflation <- 0.1
GeneDiscoveRobject <- GeneDiscoveR(overallsDir = overallsDir, N0sDir = N0sDir, dataFile = dataFile, minInflation = minInflation, maxInflation = maxInflation, stepInflation = stepInflation)
# Set active run
GeneDiscoveRobject <- set_run_active(GeneDiscoveRobject, InflationValue = 1.8)
#> -----------From OrthoFinder-----------
#> The process has been completed successfully
# Select species by phenotype
GeneDiscoveRobject <- select_species_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, columnPhenotype = "Oil-body-type", columnID = "OrthofinderID", type = "one_in_specialized_cell")
GeneDiscoveRobject <- select_species_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, columnPhenotype = "Oil-body-type", columnID = "OrthofinderID", type = "many_in_all_cells")
# Gene identification by phenotype
GeneDiscoveRobject <- gene_identification_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, formula = as.formula("one_in_specialized_cell ~ many_in_all_cells"), statistic = "Fisher", name = "PerOBtype", cores = 8)
# Select genes by phenotype
GeneDiscoveRobject <- select_genes_by_phenotype(GeneDiscoveRobject, pvalue = 0.05, oddsRatio = 1, sign = ">=", name = "PerOBtype")
# Get filtered genes table
get_filtered_genes_table(GeneDiscoveRobject, name = "PerOBtype", pvalue = 0.05, oddsRatio = 1, sign = ">=")
#> # A tibble: 1,284 × 49
#> # Rowwise:
#> HOG OG `Gene Tree Parent Clade` `1016-Treubia_lacunosa`
#> <chr> <chr> <chr> <chr>
#> 1 N0.HOG0000016 OG0000001 n147 NA
#> 2 N0.HOG0000023 OG0000001 n271 NA
#> 3 N0.HOG0000024 OG0000001 n373 jg25189.t1_0|1016
#> 4 N0.HOG0000029 OG0000001 n553 NA
#> 5 N0.HOG0000033 OG0000001 n598 NA
#> 6 N0.HOG0000046 OG0000001 n1113 NA
#> 7 N0.HOG0000047 OG0000001 n1184 NA
#> 8 N0.HOG0000050 OG0000001 n1224 NA
#> 9 N0.HOG0000054 OG0000001 n1341 NA
#> 10 N0.HOG0000057 OG0000002 n129 jg20445.t1_0|1016, jg9515.t…
#> # ℹ 1,274 more rows
#> # ℹ 45 more variables: `1017-Porella_caespitans_var_nipponica` <chr>,
#> # `1025-Porella_chinensis` <chr>, `1026-Bazzania_tridens` <chr>,
#> # `225-Ptilidium_ciliare` <chr>, `231-Lunularia_cruciata` <chr>,
#> # `302-Haplomitrium_mnioides` <chr>, `343-Odontoschisma_sphagni` <chr>,
#> # `349-Blasia_pusilla` <chr>, `359-Scapania_nepalensis` <chr>,
#> # `368-Metzgeria_furcata` <chr>, `369-Plagiochila_semidecurrens` <chr>, …