This function selects species from a GeneDiscoveR object based on a specified phenotype.
select_species_by_phenotype(
GeneDiscoveRobject = NULL,
columnPhenotype = "Oil-body-type",
columnID = "OrthofinderID",
type = NULL
)A GeneDiscoveR object containing genome data.
The name of the column in the genome data that contains the phenotype information.
The name of the column in the genome data that contains the species ID.
The specific phenotype to filter by.
The updated GeneDiscoveR object with the selected species.
# 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")
GeneDiscoveRobject <- select_species_by_phenotype(GeneDiscoveRobject = GeneDiscoveRobject, columnPhenotype = "Oil-body-type", columnID = "OrthofinderID", type = "noneOB")
# Show Phenotypes
print(GeneDiscoveRobject$Phenotypes)
#> $one_in_specialized_cell
#> [1] "1016-Treubia_lacunosa"
#> [2] "664-Conocephalum_conicum"
#> [3] "908-Cyathodium_cavernarum"
#> [4] "909-Ricciocarpos_natans"
#> [5] "952-Plagiochasma_appendiculatum"
#> [6] "231-Lunularia_cruciata"
#> [7] "MAPA-Marchantia_paleacea"
#> [8] "MpTAKv6-Marchantia_polymorpha_rudelaris"
#> [9] "MpMON-Marchantia_polymorpha_montivagans"
#> [10] "MpPOL-Marchantia_polymorpha_polymorpha"
#>
#> $many_in_all_cells
#> [1] "225-Ptilidium_ciliare"
#> [2] "1017-Porella_caespitans_var_nipponica"
#> [3] "1025-Porella_chinensis"
#> [4] "604-Gackstroemia_magellanica"
#> [5] "630-Porella_platyphylla"
#> [6] "888-Acrolejeunea_sandvicensis"
#> [7] "957-Frullania_moniliata"
#> [8] "891-Pleurozia_purpurea"
#> [9] "625-Noteroclada_confluens"
#> [10] "912-Pallavicinia_ambigua"
#> [11] "905-Metzgeria_hamata"
#> [12] "955-Jungermannia_erectum"
#> [13] "369-Plagiochila_semidecurrens"
#> [14] "1026-Bazzania_tridens"
#> [15] "343-Odontoschisma_sphagni"
#> [16] "359-Scapania_nepalensis"
#> [17] "620-Vetaforma_dusenii"
#> [18] "621-Plagiochila_sp"
#> [19] "623-Mesoptychia_sp"
#> [20] "626-Acrobolbus_urvilleanus"
#> [21] "906-Herbertus_kurzii"
#> [22] "961-Lepidozia_reptans"
#> [23] "963-Plicanthus_hirtellus"
#> [24] "965-Tetralophozia_filiformis"
#> [25] "966-Tritomaria_exsectiformis"
#> [26] "302-Haplomitrium_mnioides"
#> [27] "889-Fossombronia_cristula"
#>
#> $noneOB
#> [1] "M158-Sphaerocarpos_donnellii" "368-Metzgeria_furcata"
#> [3] "653-Riccia_cavernosa" "890-Blasia_pusilla"
#> [5] "349-Blasia_pusilla"
#>
# Output: $one_in_specialized_cell ... $many_in_all_cells ... $noneOB ...
# Clean phenotypes
GeneDiscoveRobject <- clean_phenotypes(GeneDiscoveRobject)
print(GeneDiscoveRobject$Phenotypes)
#> NULL
# Output: NULL