#' GetTraitAttributes
#' @description Wrapper of trait identification functions, including statistical validation
#' @param N Number of iterations for the random background distributions
#' @param metrics
#' @param p number of CPU threads to use simultaneously
#' @export
#' @examples
#' GetTraitAttributes()
#' GetTraitAttributes(RNAseq.data, N = 1000, p = 4)
#' @return trait.attributes.pruned
#' @author JJM van Steenbrugge
GetTraitAttributes <- function(RNAseq.data = RNAseq.data, N = 1000, metrics = distance.metrics,
p = 4, show_progres = TRUE){
if (show_progres) print("Calcluating random background for genes")
bkgd.individual <- Individual_Annotation_Background(RNAseq.data,
N = N,
metrics = metrics,
threads = p)
bkgd.individual.Zscores <- Calc_Z_scores(bkgd.individual, distance.metrics)
if (show_progres) print("Calculating random background for traits")
bkgd.traits <- Random_Trait_Background(RNAseq.data,
bkgd.individual.Zscores,
N = N,
metrics = metrics,
threads = p)
if (show_progres) print("Calculating pairwise distances between annotations")
pairwise.distances <- Calc_Pairwise_Annotation_Distance(RNAseq.data,
RNAseq.data$features$annotation.db,
metrics,
bkgd.individual.Zscores,
show.progress = F,
threads = p)
if (show_progres) print("Identifying Trait Attributes")
trait.attributes <- Identify_Trait_Attributes(RNAseq.data = RNAseq.data,
pairwise.distances = pairwise.distances,
threads = p)
if (show_progres) print("Pruning Trait Attributes")
trait.attributes.pruned <- Prune_Trait_Attributes(trait.attributes, bkgd.traits,
RNAseq.data,
p.threshold = 0.05,
pairwise.distances = metrics,bkgd.individual.Zscores = bkgd.individual.Zscores)
return(list("Traitattributes" = trait.attributes,
"Traitattributes sig" = trait.attributes.pruned,
'Random background Individual' = bkgd.individual,
'zscores individual' = bkgd.individual.Zscores,
"Random backgrounds Traits" = bkgd.traits,
"Pairwise distances" = pairwise.distances)
)
}
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