Changed default min_max_counts_per_cell to select cells with at least…

… 100 counts by default.

R/inferCNV.R

@@ -65,7 +65,7 @@ infercnv <- methods::setClass(
 #'
 #' @param max_cells_per_group maximun number of cells to use per group. Default=NULL, using all cells defined in the annotations_file. This option is useful for randomly subsetting the existing data for a quicker preview run, such as using 50 cells per group instead of hundreds.
 #' 
-#' @param min_max_counts_per_cell minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix. default=NULL and uses all cells. If used, should be set as c(min_counts, max_counts)
+#' @param min_max_counts_per_cell minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix. default=(100, +Inf) and uses all cells. If used, should be set as c(min_counts, max_counts)
 #'
 #' @param chr_exclude list of chromosomes in the reference genome annotations that should be excluded from analysis.  Default = c('chrX', 'chrY', 'chrM')
 #'
@@ -136,7 +136,7 @@ CreateInfercnvObject <- function(raw_counts_matrix,
                                  ref_group_names,
                                  delim="\t",
                                  max_cells_per_group=NULL,
-                                 min_max_counts_per_cell=NULL, # can be c(low,high) for colsums
+                                 min_max_counts_per_cell=c(100, +Inf), # can be c(low,high) for colsums
                                  chr_exclude=c('chrX', 'chrY', 'chrM') ) {
 
     ## input expression data