2.7.15 dont export interal functions, fix func name, no gitattributes

Russel88 · Mar 15, 2019 · 1a2c513 · 1a2c513
1 parent 1fb1312
commit 1a2c513
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diff --git a/.gitattributes b/.gitattributes
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DAtest
 Title: Comparing Differential Abundance/Expression Methods
-Version: 2.7.14
+Version: 2.7.15
 Authors@R: person("Jakob", "Russel",
     email = "[email protected]", 
     role = c("aut", "cre"))

diff --git a/NAMESPACE b/NAMESPACE
@@ -41,7 +41,6 @@ export(DA.mva)
 export(DA.neb)
 export(DA.pea)
 export(DA.per)
-export(DA.phyloseq)
 export(DA.poi)
 export(DA.qpo)
 export(DA.qua)
@@ -56,17 +55,13 @@ export(DA.zig)
 export(DA.znb)
 export(DA.zpo)
 export(DA.zzz)
-export(add.tax.DA)
 export(allDA)
 export(featurePlot)
-export(gm_mean)
 export(norm_alr)
 export(norm_clr)
 export(powerDA)
 export(preDA)
-export(pruneTests)
 export(runtimeDA)
-export(spikein)
 export(testDA)
 export(vennDA)
 import(MASS)

diff --git a/R/DA.adx.R b/R/DA.adx.R
@@ -41,7 +41,7 @@ DA.adx <- function(data, predictor, ...){
     x[!is.na(x$effect) & x$effect < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2])
     x$Feature <- rownames(x)
 
-    if(class(data) == "phyloseq") x <- add.tax.DA(data, x)
+    if(class(data) == "phyloseq") x <- addTax(data, x)
 
     return(x)
   } else {

diff --git a/R/DA.aoa.R b/R/DA.aoa.R
@@ -69,7 +69,7 @@ DA.aoa <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, all
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "ANOVA - ALR (aoa)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.aoc.R b/R/DA.aoc.R
@@ -67,7 +67,7 @@ DA.aoc <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 1, all
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "ANOVA - CLR (aoc)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.aov.R b/R/DA.aov.R
@@ -67,7 +67,7 @@ DA.aov <- function(data, predictor, covars = NULL, relative = TRUE, p.adj = "fdr
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "ANOVA (aov)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.bay.R b/R/DA.bay.R
@@ -57,7 +57,7 @@ DA.bay <- function(data, predictor, allResults = FALSE, ...){
 
     output_df$Method <- "baySeq (bay)"
 
-    if(class(data) == "phyloseq") output_df <- add.tax.DA(data, output_df)
+    if(class(data) == "phyloseq") output_df <- addTax(data, output_df)
 
     if(allResults) return(CD) else return(output_df)
   } else {

diff --git a/R/DA.ds2.R b/R/DA.ds2.R
@@ -126,7 +126,7 @@ DA.ds2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     res$Feature <- DESeq2::results(x)@rownames
     res$Method <- "DESeq2 man. geoMeans (ds2)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(x) else return(res)
   } else {

diff --git a/R/DA.ds2x.R b/R/DA.ds2x.R
@@ -118,7 +118,7 @@ DA.ds2x <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL
     res$Feature <- DESeq2::results(x)@rownames
     res$Method <- "DESeq2 (ds2x)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(x) else return(res)  
   } else {

diff --git a/R/DA.ere.R b/R/DA.ere.R
@@ -59,7 +59,7 @@ DA.ere <- function(data, predictor, p.adj = "fdr", ...){
     ta$Feature <- rownames(ta)
     ta$Method <- "EdgeR exact - TMM (ere)"
 
-    if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta)
+    if(class(data) == "phyloseq") ta <- addTax(data, ta)
 
     return(ta) 
 

diff --git a/R/DA.ere2.R b/R/DA.ere2.R
@@ -58,7 +58,7 @@ DA.ere2 <- function(data, predictor, p.adj = "fdr", ...){
     ta$Feature <- rownames(ta)
     ta$Method <- "EdgeR exact - RLE (ere2)"
 
-    if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta)
+    if(class(data) == "phyloseq") ta <- addTax(data, ta)
 
     return(ta) 
   } else {

diff --git a/R/DA.erq.R b/R/DA.erq.R
@@ -109,7 +109,7 @@ DA.erq <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     ta$Feature <- rownames(ta)
     ta$Method <- "EdgeR qll - TMM (erq)"
 
-    if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta)
+    if(class(data) == "phyloseq") ta <- addTax(data, ta)
 
     if(allResults) return(qlf) else return(ta)
 

diff --git a/R/DA.erq2.R b/R/DA.erq2.R
@@ -109,7 +109,7 @@ DA.erq2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL
     ta$Feature <- rownames(ta)
     ta$Method <- "EdgeR qll - RLE (erq2)"
 
-    if(class(data) == "phyloseq") ta <- add.tax.DA(data, ta)
+    if(class(data) == "phyloseq") ta <- addTax(data, ta)
 
     if(allResults) return(qlf) else return(ta)
 

diff --git a/R/DA.fri.R b/R/DA.fri.R
@@ -62,7 +62,7 @@ DA.fri <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr
     res$Feature <- gsub(".Friedman.*","",rownames(res))
     res$Method <- "Friedman (fri)" 
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     return(res)
   }

diff --git a/R/DA.kru.R b/R/DA.kru.R
@@ -54,7 +54,7 @@ DA.kru <- function(data, predictor, relative = TRUE, p.adj = "fdr", allResults =
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Kruskal-Wallis (kru)" 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 

diff --git a/R/DA.lao.R b/R/DA.lao.R
@@ -65,7 +65,7 @@ DA.lao <- function(data, predictor, covars = NULL, relative = TRUE, p.adj = "fdr
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Log ANOVA (lao)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.lao2.R b/R/DA.lao2.R
@@ -64,7 +64,7 @@ DA.lao2 <- function(data, predictor, covars = NULL, p.adj = "fdr", delta = 0.001
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Log ANOVA 2 (lao2)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.lia.R b/R/DA.lia.R
@@ -104,7 +104,7 @@ DA.lia <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     res$Feature <- rownames(res)
     res$Method <- "LIMMA - ALR (lia)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(fit.eb) else return(res) 
 

diff --git a/R/DA.lic.R b/R/DA.lic.R
@@ -104,7 +104,7 @@ DA.lic <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     res$Feature <- rownames(res)
     res$Method <- "LIMMA - CLR (lic)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(fit.eb) else return(res) 
 

diff --git a/R/DA.lim.R b/R/DA.lim.R
@@ -105,7 +105,7 @@ DA.lim <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$Feature <- rownames(res)
     res$Method <- "LIMMA (lim)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(fit.eb) else return(res)
 

diff --git a/R/DA.lli.R b/R/DA.lli.R
@@ -103,7 +103,7 @@ DA.lli <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$Feature <- rownames(res)
     res$Method <- "Log LIMMA (lli)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(fit.eb) else return(res) 
 

diff --git a/R/DA.lli2.R b/R/DA.lli2.R
@@ -103,7 +103,7 @@ DA.lli2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL
     res$Feature <- rownames(res)
     res$Method <- "Log LIMMA 2 (lli2)"
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
 
     if(allResults) return(fit.eb) else return(res) 
 

diff --git a/R/DA.llm.R b/R/DA.llm.R
@@ -156,7 +156,7 @@ DA.llm <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Log Linear reg. (llm)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   } 
 

diff --git a/R/DA.llm2.R b/R/DA.llm2.R
@@ -155,7 +155,7 @@ DA.llm2 <- function(data, predictor, paired = NULL, covars = NULL, out.all = NUL
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Log Linear reg. 2 (llm2)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }  
 }
diff --git a/R/DA.lma.R b/R/DA.lma.R
@@ -159,7 +159,7 @@ DA.lma <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Linear model - ALR (lma)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   } 
 

diff --git a/R/DA.lmc.R b/R/DA.lmc.R
@@ -158,7 +158,7 @@ DA.lmc <- function(data, predictor, paired = NULL, covars = NULL, out.all = NULL
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Linear model - CLR (lmc)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   } 
 

diff --git a/R/DA.lrm.R b/R/DA.lrm.R
@@ -154,7 +154,7 @@ DA.lrm <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$pval.adj <- p.adjust(res$pval, method = p.adj)
     res$Feature <- rownames(res)
     res$Method <- "Linear regression (lrm)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 

diff --git a/R/DA.ltt.R b/R/DA.ltt.R
@@ -82,7 +82,7 @@ DA.ltt <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr
     res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2])
     res$Feature <- rownames(res)
     res$Method <- "Log t-test (ltt)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }

diff --git a/R/DA.ltt2.R b/R/DA.ltt2.R
@@ -81,7 +81,7 @@ DA.ltt2 <- function(data, predictor, paired = NULL, p.adj = "fdr", delta = 0.001
     res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2])
     res$Feature <- rownames(res)
     res$Method <- "Log t-test2 (ltt2)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }
diff --git a/R/DA.msf.R b/R/DA.msf.R
@@ -61,7 +61,7 @@ DA.msf <- function(data, predictor, p.adj = "fdr", allResults = FALSE, ...){
     temp_table[!is.na(temp_table$logFC) & temp_table$logFC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2])
     temp_table$Method <- "MgSeq Feature (msf)"  
 
-    if(class(data) == "phyloseq") temp_table <- add.tax.DA(data, temp_table)
+    if(class(data) == "phyloseq") temp_table <- addTax(data, temp_table)
 
     if(allResults) return(mgsfit) else return(temp_table)
 

diff --git a/R/DA.mva.R b/R/DA.mva.R
@@ -105,7 +105,7 @@ DA.mva <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
       res$Feature <- rownames(pvals.unadj$uni.test)
       res$Method <- "mvabund (mva)"
 
-      if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+      if(class(data) == "phyloseq") res <- addTax(data, res)
 
       return(res)
     }

diff --git a/R/DA.neb.R b/R/DA.neb.R
@@ -211,7 +211,7 @@ DA.neb <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$Method <- "Negbinom GLM (neb)"
 
     if(nrow(res) > 1){
-      if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+      if(class(data) == "phyloseq") res <- addTax(data, res)
     }
     return(res)
   } else {

diff --git a/R/DA.pea.R b/R/DA.pea.R
@@ -54,7 +54,7 @@ DA.pea <- function(data, predictor, relative = TRUE, p.adj = "fdr", ...){
   res$Method <- "Pearson (pea)"
 
   # Add tax table if available
-  if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+  if(class(data) == "phyloseq") res <- addTax(data, res)
 
   return(res)  
 }

diff --git a/R/DA.per.R b/R/DA.per.R
@@ -125,7 +125,7 @@ DA.per <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr
   output_df$pval.adj <- p.adjust(output_df$pval, method = p.adj)
   output_df$Method <- "Permutation (per)"
 
-  if(class(data) == "phyloseq") output_df <- add.tax.DA(data, output_df)
+  if(class(data) == "phyloseq") output_df <- addTax(data, output_df)
 
   return(output_df)
 }

diff --git a/R/DA.phyloseq.R b/R/DA.phyloseq.R
@@ -1,14 +1,3 @@
-#' Extract data from a \code{phyloseq} object to be used in \code{DAtest}
-#' 
-#' Internal function
-#' 
-#' @param data A \code{phyloseq} object
-#' @param predictor The \code{predictor} of interest
-#' @param paired Factor for paired/blocked experimental designs.
-#' @param covars A character vector with names of the variables in \code{sample_data(data)}
-#' @return A list with data extracted from the \code{phyloseq} object
-#' @export
-
 DA.phyloseq <- function(data, predictor, paired = NULL, covars = NULL){
 
   ok <- tryCatch({

diff --git a/R/DA.poi.R b/R/DA.poi.R
@@ -245,7 +245,7 @@ DA.poi <- function(data, predictor, paired = NULL, covars = NULL, relative = TRU
     res$Method <- "Poisson GLM (poi)"
 
     if(nrow(res) > 1){
-      if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+      if(class(data) == "phyloseq") res <- addTax(data, res)
     }
     return(res)
   }

diff --git a/R/DA.qpo.R b/R/DA.qpo.R
@@ -158,7 +158,7 @@ DA.qpo <- function(data, predictor, covars = NULL, relative = TRUE, out.all = NU
     res$Method <- "Quasi-Poisson GLM (qpo)"
 
     if(nrow(res) > 1){
-      if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+      if(class(data) == "phyloseq") res <- addTax(data, res)
     }
     return(res)
   }

diff --git a/R/DA.qua.R b/R/DA.qua.R
@@ -64,7 +64,7 @@ DA.qua <- function(data, predictor, paired = NULL, relative = TRUE, p.adj = "fdr
     res$Feature <- gsub(".Quade.*","",rownames(res))
     res$Method <- "Quade (qua)" 
 
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 

diff --git a/R/DA.sam.R b/R/DA.sam.R
@@ -99,7 +99,7 @@ DA.sam <- function(data, predictor, paired = NULL, fdr.output = 0.05, allResults
 
     df$Method <- "SAMseq (sam)"
 
-    if(class(data) == "phyloseq") df <- add.tax.DA(data, df)
+    if(class(data) == "phyloseq") df <- addTax(data, df)
 
     if(allResults){
       return(res)

diff --git a/R/DA.spe.R b/R/DA.spe.R
@@ -51,7 +51,7 @@ DA.spe <- function(data, predictor, relative = TRUE, p.adj = "fdr", ...){
   res$Feature <- rownames(res)
   res$Method <- "Spearman (spe)"
 
-  if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+  if(class(data) == "phyloseq") res <- addTax(data, res)
 
   return(res)  
 }

diff --git a/R/DA.tta.R b/R/DA.tta.R
@@ -86,7 +86,7 @@ DA.tta <- function(data, predictor, paired = NULL, p.adj = "fdr", delta = 1, tes
     res[!is.na(res$log2FC) & res$log2FC < 0,"ordering"] <- paste0(levels(as.factor(predictor))[1],">",levels(as.factor(predictor))[2])
     res$Feature <- rownames(res)
     res$Method <- "t-test - ALR (tta)"
-    if(class(data) == "phyloseq") res <- add.tax.DA(data, res)
+    if(class(data) == "phyloseq") res <- addTax(data, res)
     return(res)
   }
 }