diff --git a/R/getCellbase-methods.R b/R/getCellbase-methods.R index 064a5a3f..b10b8555 100644 --- a/R/getCellbase-methods.R +++ b/R/getCellbase-methods.R @@ -37,8 +37,8 @@ setMethod("getCellBase", "CellBaseR", definition = function(object, category, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } # TODO: param are not enabled diff --git a/R/getGene-methods.R b/R/getGene-methods.R index 669f089b..dd25c053 100644 --- a/R/getGene-methods.R +++ b/R/getGene-methods.R @@ -35,8 +35,8 @@ setMethod("getGene", "CellBaseR", definition = function(object, ids, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } # TODO: param are not enabled diff --git a/R/getProtein-methods.R b/R/getProtein-methods.R index db3ec682..943e24f9 100644 --- a/R/getProtein-methods.R +++ b/R/getProtein-methods.R @@ -34,8 +34,8 @@ setMethod("getProtein", "CellBaseR", definition = function(object, ids, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } result <- fetchCellbase(object=object, file=NULL, meta=NULL, categ=categ, diff --git a/R/getRegion-methods.R b/R/getRegion-methods.R index faedc391..9e9038f2 100644 --- a/R/getRegion-methods.R +++ b/R/getRegion-methods.R @@ -31,7 +31,7 @@ setMethod("getRegion", "CellBaseR", definition = function(object, ids, resource, if (!is.null(param)){ param <- c(genome=param@genome, gene=param@gene, region=param@region, rs=param@rs,so=param@so, - phenotype=param@phenotype, limit=param@limit, + phenotype=param@phenotype, include=param@include, exclude=param@exclude, limit=param@limit) param <- paste(param, collapse = "&") diff --git a/R/getTranscript-methods.R b/R/getTranscript-methods.R index dd28a791..1e43d230 100644 --- a/R/getTranscript-methods.R +++ b/R/getTranscript-methods.R @@ -35,8 +35,8 @@ setMethod("getTranscript", "CellBaseR", definition = function(object, ids, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } result <- fetchCellbase(object=object, file=NULL, meta=NULL, categ=categ, diff --git a/R/getVariant-methods.R b/R/getVariant-methods.R index 8e11fec2..9930043c 100644 --- a/R/getVariant-methods.R +++ b/R/getVariant-methods.R @@ -41,8 +41,8 @@ setMethod("getVariant", "CellBaseR", definition = function(object, ids, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } diff --git a/R/getXref-methods.R b/R/getXref-methods.R index 91375497..f422e778 100644 --- a/R/getXref-methods.R +++ b/R/getXref-methods.R @@ -36,8 +36,8 @@ setMethod("getXref", "CellBaseR", definition = function(object, ids, resource, clinsig_labels=param@clinsig_labels, alleleOrigin=param@alleleOrigin, consistency_labels=param@consistency_labels, - limit=param@limit, include=param@include, - exclude=param@exclude, limit=param@limit) + include=param@include, exclude=param@exclude, + limit=param@limit) param <- paste(param, collapse = "&") } result <- fetchCellbase(object=object, file=NULL, meta=NULL, categ=categ,