From fc33baf4705e1dfe917460f9c57e55555fb00565 Mon Sep 17 00:00:00 2001 From: Augustine Amakiri Date: Tue, 22 Mar 2022 17:33:10 -0600 Subject: [PATCH] Fixed the error with building the vignettes and reslovethe error with the nanopipeline preDE and DE modules --- R/NBthDE.R | 2 +- R/NBthDE_nllopt.R | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/R/NBthDE.R b/R/NBthDE.R index 6402e4d..68419bc 100644 --- a/R/NBthDE.R +++ b/R/NBthDE.R @@ -372,7 +372,7 @@ setMethod( for (iter in seq_len(iterations)) { if (iter == 1) { result <- NBthDE_paraOptall( - t(object[features_high, ]), X, sizefact_BG, sizefact, + t(object[features_high, ]), as.matrix(X), sizefact_BG, sizefact, preci1, threshold_mean * probenum[features_high], preci2, startpara, sizescalebythreshold, (iter == iterations) ) diff --git a/R/NBthDE_nllopt.R b/R/NBthDE_nllopt.R index c4cd9de..6a90075 100644 --- a/R/NBthDE_nllopt.R +++ b/R/NBthDE_nllopt.R @@ -1,10 +1,4 @@ - - - - - - NBthDE_scalenll <- function(X, Y, probenum, regcoefmat, rvec, sizefact0, threshold, sizescale, threshold_mean) { tmp0 <- 2^(X %*% regcoefmat) if (sizescale) {