diff --git a/R/differential.R b/R/differential.R index 812b5704..c797eec8 100644 --- a/R/differential.R +++ b/R/differential.R @@ -182,7 +182,7 @@ diff_expression <- function(object, is_hermes_data(object), is.string(group) ) - expect_factor(colData(object)[[group]], n.levels = 2L) + assert_factor(colData(object)[[group]], n.levels = 2) method <- match.arg(method, c("voom", "deseq2")) @@ -256,7 +256,7 @@ setMethod( definition = function(object, adj_p_val_thresh = 0.05, log2_fc_thresh = 2.5) { - expect_proportion(adj_p_val_thresh) + assert_proportion(adj_p_val_thresh) assert_that( is.number(log2_fc_thresh), log2_fc_thresh > 0 diff --git a/R/graphs.R b/R/graphs.R index 9c55e6cf..4d1a7c4f 100644 --- a/R/graphs.R +++ b/R/graphs.R @@ -149,7 +149,7 @@ draw_nonzero_boxplot <- function(object, is_hermes_data(object), is_class(position, "Position") ) - expect_proportion(alpha) + assert_proportion(alpha) no_na_count <- colSums(counts(object) != 0) df <- data.frame(no_na = no_na_count, x = "Sample") diff --git a/R/quality.R b/R/quality.R index ebbb9e5f..e4071669 100644 --- a/R/quality.R +++ b/R/quality.R @@ -36,9 +36,9 @@ control_quality <- function(min_cpm = 1, assert_that( is.number(min_cpm) && min_cpm >= 0 ) - expect_proportion(min_cpm_prop) - expect_proportion(min_corr) - expect_count(min_depth, positive = TRUE, null.ok = TRUE) + assert_proportion(min_cpm_prop) + assert_proportion(min_corr) + assert_numeric(min_depth, lower = 0, null.ok = TRUE, len = 1) list( min_cpm = min_cpm, diff --git a/man/h_all_duplicated.Rd b/man/h_all_duplicated.Rd index 1538b745..6246a9aa 100644 --- a/man/h_all_duplicated.Rd +++ b/man/h_all_duplicated.Rd @@ -7,7 +7,8 @@ h_all_duplicated(x) } \arguments{ -\item{x}{a vector or a data frame or an array or \code{NULL}.} +\item{x}{a (generalized, see \code{\link[base]{is.vector}}) vector, a data + frame, an array or \code{NULL}.} } \value{ Logical vector flagging all occurrences of duplicate values as \code{TRUE}.