get_significant_genes: Get the dataframe with the significant genes

In trvinh/test: PhyloProfile

Description

Get the dataframe with the significant genes

Usage

get_significant_genes(in_group, selected_genes_list, rank, var,
    use_common_ancestor, reference_taxon, parameters, ncbi_id_list, 
    data_full, right_format_features, domains)

Arguments

in_group	list of taxa
selected_genes_list	list of genes
rank	selected taxonamy rank
var	variable for which to calculate the significance
use_common_ancestor	boolean if the common anchestor should be used
reference_taxon	taxon which is used as reference
parameters	contains "show_p_value","highlight_significant", "significance", "var1_id", "var2_id", "x_size_gc", "y_size_gc", "interesting_features", "angle_gc", "legend_gc", "legend_size_gc"
ncbi_id_list	list of ncbi ids
data_full	full processed main data
right_format_features	boolean if the features have the right format
domains	dataframe holding the domain input

Value

dataframe with the significant genes

Author(s)

Carla Mölbert ([e-mail])

Examples

data("main_long_raw", package="phyloprofile")
data("full_processed_profile", package="phyloprofile")
in_group <- c("Aeropyrum pernix", "Agrobacterium fabrum")
selected_genes_list <- "OG_1017"
rank <- "species"
var <- ""
use_common_ancestor <- FALSE
reference_taxon <- "Homo sapiens"
ncbi_id_list <- get_input_taxa_id(main_long_raw)
data_full <- full_processed_profile
right_format_features <- TRUE
domain_file <- system.file(
    "extdata", "domain_files/OG_1017.domains",
    package = "phyloprofile", mustWork = TRUE
)
domains <- parse_domain_input("OG_1017", domain_file, "file")
parameters <- list(
    "show_p_value" = TRUE,
    "highlight_significant" = FALSE,
    "significance" = 0.05,
    "var1_id" = "1st variable",
    "var2_id" = "2nd variable",
    "x_size_gc" = 9,
    "y_size_gc" = 9,
    "interesting_features" = NULL,
    "angle_gc" = 90,
    "legend_gc" = "none",
    "legend_size_gc" = 9,
    "p_values_size" = 9
)
get_significant_genes(
    in_group,
    selected_genes_list,
    rank,
    var,
    use_common_ancestor,
    reference_taxon,
    parameters,
    ncbi_id_list,
    data_full,
    right_format_features,
    domains
)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.