update docs and fix conditional in msImpute

soroorh · soroorh · commit 35c4a29127f6 · 2025-03-16T00:06:21.000+11:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,7 @@ License: GPL (>=2)
 Encoding: UTF-8
 LazyData: true
 BugReports: https://github.com/DavisLaboratory/msImpute/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
 Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
 VignetteBuilder: knitr
 biocViews: MassSpectrometry, Proteomics, Software
diff --git a/R/msImpute.R b/R/msImpute.R
@@ -82,7 +82,7 @@ msImpute <- function(y, method=c("v2-mnar", "v2", "v1"),
 	  
 	  stop("Peptides with excessive NAs are detected. Please revisit your fitering step (at least 4 non-missing measurements are required for any peptide) or set relax_min_obs=TRUE.")
   }
-  ifelse(!relax_min_obs & any(rowSums(!is.na(y)) <= 3)){
+  else if(!relax_min_obs & any(rowSums(!is.na(y)) <= 3)){
 	  critical_obs <- which(rowSums(!is.na(y)) <= 3)
 	  message("Features with less than 4 non-missing measurements detected. These will be treated as MNAR.")
   }else{
diff --git a/man/msImpute.Rd b/man/msImpute.Rd

Original file line number	Diff line number	Diff line change
`@@ -82,7 +82,7 @@ msImpute <- function(y, method=c("v2-mnar", "v2", "v1"),`
`82`	`82`
`83`	`83`	`stop("Peptides with excessive NAs are detected. Please revisit your fitering step (at least 4 non-missing measurements are required for any peptide) or set relax_min_obs=TRUE.")`
`84`	`84`	`}`
`85`		`- ifelse(!relax_min_obs & any(rowSums(!is.na(y)) <= 3)){`
	`85`	`+ else if(!relax_min_obs & any(rowSums(!is.na(y)) <= 3)){`
`86`	`86`	`critical_obs <- which(rowSums(!is.na(y)) <= 3)`
`87`	`87`	`message("Features with less than 4 non-missing measurements detected. These will be treated as MNAR.")`
`88`	`88`	`}else{`