fix makeGoSet example

R/makeGoSet.R

@@ -1,5 +1,5 @@
 ##' The function pulls the gene ontology (GO) terms
-##' for a set of feature names. 
+##' for a set of feature names.
 ##'
 ##' @title Retrieve GO terms for feature names
 ##' @param id An \code{character} with feature names to be pulled from
@@ -104,7 +104,7 @@ getGOFromFeatures <- function(id,
 ##' goset <- makeGoSet(dunkley2006[1:10, ],
 ##' dunkley2006params)
 ##' goset
-##' exprs(goset)[1:10, 1:5]
+##' exprs(goset)
 ##' image(goset)
 makeGoSet <- function(object, params,
  namespace = "cellular_component",
@@ -130,12 +130,12 @@ makeGoSet <- function(object, params,
  evidence = evidence)
  attrs <- chooseAttributesX(params)
  l <- lapply(fn,
- function(x) godf[godf[, params@filter] == x, attrs[1]]) 
+ function(x) godf[godf[, params@filter] == x, attrs[1]])
  allgo <- unique(unlist(l))
  gomat <- matrix(0, length(fn), length(allgo))
  rownames(gomat) <- fn
  colnames(gomat) <- allgo
- for (i in 1:nrow(gomat)) 
+ for (i in 1:nrow(gomat))
  gomat[i, l[[i]]] <- 1
  goset <- new("MSnSet",
  exprs = gomat)
@@ -144,6 +144,5 @@ makeGoSet <- function(object, params,
  msg <- paste0("Constructed GO set using ", namespace, " namespace")
  goset <- MSnbase:::logging(goset, msg)
  if (validObject(goset))
- return(goset) 
+ return(goset)
 }
-