fix

DESCRIPTION

@@ -27,7 +27,7 @@ RoxygenNote: 7.1.1
 BugReports: https://github.com/rezakj/iCellR/issues
 URL: https://github.com/rezakj/iCellR
 NeedsCompilation: yes
-Packaged: 2021-10-07 18:26:50 UTC; khodaa01
+Packaged: 2021-11-09 17:46:10 UTC; khodaa01
 Author: Alireza Khodadadi-Jamayran [aut, cre]
     (<https://orcid.org/0000-0003-2495-7504>),
   Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),

R/F0021.R

@@ -5,6 +5,7 @@
 #' @param data.type Choose from "main", "atac", "atac.imputed" and "imputed", default = "main"
 #' @param conds.to.avg Choose the conditions you want to average, default = NULL (all conditions).
 #' @param rounding.digits integer indicating the number of decimal places (round) or significant digits (signif) to be used.
+#' @param low.cell.filt filter out clusters with low number of cells, default = 5.
 #' @param round.num Rounding of Numbers, default = FALSE.
 #' @return An object of class iCellR.
 #' @import progress
@@ -13,6 +14,7 @@ clust.avg.exp <- function (x = NULL,
                            data.type = "main",
                            conds.to.avg = NULL,
                            rounding.digits = 4,
+                           low.cell.filt = 5,
                            round.num = FALSE) {
   if ("iCellR" != class(x)[1]) {
     stop("x should be an object of class iCellR")
@@ -35,6 +37,21 @@ clust.avg.exp <- function (x = NULL,
   sampleCondition <- DATA$clusters
   conditions <- sort(unique(sampleCondition))
   DATA1 <- DATA
+#### warn and filter
+  warn <- as.data.frame(table(DATA1$clusters))
+  warn <- subset(warn, warn$Freq < low.cell.filt)
+  warn <- as.numeric(as.matrix(warn$Var1))
+  if(length(warn) != 0) {
+    message("########### Warning ###########")
+    message("###############################")
+    message("###############################")
+    message(paste("#### Filter warning: cluster",warn,"has less than",ncell.filt,"cells (cluster excluded)"))
+    DATA1<- subset(DATA1,!DATA1$clusters %in% warn)
+    conditions <- subset(conditions, !conditions %in% warn)
+    message("###############################")
+    message("###############################")
+    message("###############################")
+  }
   ## get main data
   if (data.type == "main") {
     Table <- x@main.data

R/F0049.R

@@ -4,7 +4,7 @@
 #' @param object A data frame containing gene counts for cells.
 #' @param scoring.List Genes that are used as a marker for phases.
 #' @param return.stats Return the data or object. If FALSE the object would be returned.
-#' @param scoring.method Choose from "coverage" or "tirosh" for scoring method. See: https://science.sciencemag.org/content/352/6282/189
+#' @param scoring.method Choose from "coverage" or "tirosh" for scoring method.
 #' @return The data frame object
 #' @importFrom Hmisc cut2
 #' @export

R/F0051.R

@@ -3,5 +3,5 @@
 #' A dataset containing the genes for S phase
 #'
 #' @format A character with 43 genes
-#' @source \url{https://science.sciencemag.org/content/352/6282/189}
+#' @source \url{https://www.science.org/doi/abs/10.1126/science.aad0501}
 "s.phase"

R/F0053.R

@@ -3,5 +3,5 @@
 #' A dataset containing the genes for G2 and M phase
 #'
 #' @format A character with 54 genes
-#' @source \url{https://science.sciencemag.org/content/352/6282/189}
+#' @source \url{https://www.science.org/doi/abs/10.1126/science.aad0501}
 "g2m.phase"

R/F0071.R

@@ -5,7 +5,7 @@
 #' @param data.type Choose from "raw.data" or "main.data", "imputed.data", default = "main.data".
 #' @param scoring.List Genes that are used as a marker for phases.
 #' @param return.stats Return the data or object. If FALSE the object would be returned.
-#' @param scoring.method Choose from "tirosh (Tirosh, et. al. 2016), mean, sum, gsva, ssgsea, zscore and plage. , default = "tirosh". See: https://science.sciencemag.org/content/352/6282/189
+#' @param scoring.method Choose from "tirosh (Tirosh, et. al. 2016), mean, sum, gsva, ssgsea, zscore and plage. , default = "tirosh".
 #' @return The data frame object
 #' @importFrom Hmisc cut2
 #' @export