fix misspelled variable

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SigGenes
 Title: Automated differential analysis and signature generation for bulk and single-cell data
 Description: Automated differential analysis between groups based on limma-voom and generation of per-group signatures via custom filtering.
-Version: 1.0.1
+Version: 1.0.2
 Author: Alexander Bender [aut,cre]
 Maintainer: Alexander Bender <[email protected]>
 License: LGPL (>=2)

R/de_testing.R

@@ -43,12 +43,16 @@
 #' sce$donor <- rep(LETTERS[1:4], 250)
 #' res_pairwise <- de_limma(x = sce, aggregate_by = c("group", "donor"),
 #'                          main_covariate = "group", other_covariates = c("donor"))
+#'
 #' res_pairwise_block <- de_limma(x = sce, aggregate_by = c("group", "donor"),
 #'                                main_covariate = "group", block = "donor")
+#'
 #' res_average <- de_limma(x = sce, aggregate_by = c("group", "donor"),
 #'                         main_covariate = "group", other_covariates = c("donor"),
 #'                         mode="average")
 #'
+#' res_singlecell <- de_limma(x = sce, main_covariate = "group")
+#'
 #' @author Alexander Bender
 #'
 #' @references
@@ -130,9 +134,9 @@ de_limma <- function(x, use_assay = "counts", aggregate_by=NULL, use_existing_sf
     sf <- suppressWarnings(sizeFactors(x))
     # scran::convertTo()
     if (!is.null(sf)) {
-      nf <- log(sf/y$samples$lib.size)
+      nf <- log(sf/pb$samples$lib.size)
       nf <- exp(nf - mean(nf))
-      y$samples$norm.factors <- nf
+      pb$samples$norm.factors <- nf
     }
 
     if(use_existing_sf){