diff --git a/R/external.R b/R/external.R index 47b4f26..1ef6c4a 100644 --- a/R/external.R +++ b/R/external.R @@ -8,6 +8,11 @@ #' @param keyType key type of gene #' @param argList argument list to pass to refseq() #' @export +#' @examples +#' cols <- sample(c(1), 6, replace=TRUE) +#' names(cols) <- c("PNKP","ERCC2","ERCC3","IRF3","TP53","MCM6") +#' wg <- list("colors"=cols) +#' refseqWGCNA(wg, keyType="SYMBOL") #' @return list of biotext class object refseqWGCNA <- function(wgcna, keyType="ENSEMBL", argList=list()) { all_cols <- unique(wgcna$colors) diff --git a/R/steps.R b/R/steps.R index bb88b62..3049ed1 100644 --- a/R/steps.R +++ b/R/steps.R @@ -71,7 +71,10 @@ obtain_alliance <- function(geneList, file="GENE-DESCRIPTION-TSV_HUMAN.tsv", #' @param curate curated articles (TRUE) or search for PubMed (FALSE) #' if FALSE, same for fetching from PubMed by specified query #' @export -#' @examples obtain_bugsigdb("Veillonella dispar") +#' @examples +#' \dontrun{ +#' obtain_bugsigdb("Veillonella dispar") +#' } #' @return biotext class object obtain_bugsigdb <- function(mb_list, target="title", diff --git a/man/obtain_bugsigdb.Rd b/man/obtain_bugsigdb.Rd index d6823c0..6487059 100644 --- a/man/obtain_bugsigdb.Rd +++ b/man/obtain_bugsigdb.Rd @@ -26,7 +26,9 @@ Obtain microbe-related information from bugsigdb Obtain microbe description from BugSigDB using bugsigdbr. } \examples{ -obtain_bugsigdb("Veillonella dispar") +\dontrun{ + obtain_bugsigdb("Veillonella dispar") +} } \seealso{ generalf diff --git a/man/refseqWGCNA.Rd b/man/refseqWGCNA.Rd index ffbb422..2908772 100644 --- a/man/refseqWGCNA.Rd +++ b/man/refseqWGCNA.Rd @@ -22,3 +22,9 @@ Text mining WGCNA results \details{ Return the list of biotext class object per cluster for the blockwise module results in WGCNA } +\examples{ +cols <- sample(c(1), 6, replace=TRUE) +names(cols) <- c("PNKP","ERCC2","ERCC3","IRF3","TP53","MCM6") +wg <- list("colors"=cols) +refseqWGCNA(wg, keyType="SYMBOL") +}