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name space issue
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change it
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ZW-xjtlu committed Apr 21, 2018
1 parent c0e8ee4 commit 8936eb6
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10 changes: 9 additions & 1 deletion NAMESPACE
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exportPattern("^[[:alpha:]]+")
# Generated by roxygen2: do not edit by hand

export(GOEA)
export(GOslimEA)
export(exact2slim)
export(gene2go)
importFrom(AnnotationDbi,select)
importFrom(GSEABase,GOCollection)
importFrom(GSEABase,goSlim)
2 changes: 1 addition & 1 deletion R/GOEA.R
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#' @param pvalue_correction method used for multiple hypothesis adjustment, can be one in "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", and "none".
#' @param interpret_term whether to let the GO term readable, default FALSE.
#' @param show_gene_name whether to attach readable gene names for each GO term, default FALSE.
#' @importFrom select AnnotationDbi
#' @importFrom AnnotationDbi select
#' @export
GOEA <- function(gene_set,
back_ground,
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3 changes: 1 addition & 2 deletions R/exact2slim.R
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#' @param Unique wheather to unique the mapped GO slim term of each GO exact term.
#' @return a \code{data.frame} indicating the mapping index between query GO exact terms and its GO slim terms.
#'
#' @importFrom goSlim GSEABase
#' @importFrom GOCollection GSEABase
#' @importFrom GSEABase goSlim GOCollection
#' @export
exact2slim <- function(Exact_terms,
Slim_collection = NULL,
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2 changes: 1 addition & 1 deletion R/gene2go.R
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#' @param OrgDB an \code{OrgDb} object defined by AnnotationDbi.
#' @param Category a character specifying the gene ontology category, can be one in "BP", "CC", and "MF", default "BP".
#' @param Drop_zero_match whether to drop the genes that mapped to no terms at all, default FALSE.
#' @importFrom select AnnotationDbi
#' @importFrom AnnotationDbi select
#' @export
gene2go <- function(Gene_ID,
Gene_key_type = "ENTREZID",
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