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Update Allstats.R
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@CHKim5
CHKim5 committed Jul 29, 2021
1 parent babee5c commit 9b93cf2
Showing 1 changed file with 43 additions and 38 deletions.
81 changes: 43 additions & 38 deletions R/Allstats.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,21 @@
#'
Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
{

LETTERS702 <- c(sapply(LETTERS, function(x) paste0(x, LETTERS)))
LETTERS37232 <- c(LETTERS, LETTERS702, sapply(LETTERS, function(x) paste0(x,
LETTERS702)))
LETTERS37232 <- LETTERS37232[-365]
LETTERS210729 <- c(LETTERS, LETTERS702,LETTERS37232, sapply(LETTERS, function(x) paste0(x,
LETTERS37232)))
LETTERS210729 <- LETTERS210729[-365]
LETTERS210729<-LETTERS210729[-10205]
LETTERS210729<-LETTERS210729[-267101]
colnames(Data) <- Data[1, ]
Data <- Data[-1, -2]
Data<-Data %>% dplyr::arrange(Group)
Data_renamed <- Data
nmet <- ncol(Data) - 2
colnames(Data_renamed) <- c(colnames(Data[1:2]), LETTERS37232[1:nmet])
colnames(Data_renamed) <- c(colnames(Data[1:2]), LETTERS210729[1:nmet])
rownames(Data_renamed) <- Data[, 1]
Data_renamed_raw <- Data_renamed[, -c(1, 2)]
Data_renamed_raw <- apply(Data_renamed_raw, 2, as.numeric)
Expand All @@ -45,14 +50,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
else {
for (met in 1:(ncol(Data) - 2)) {
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
"T_test", sep = "_"), t.test(x = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_1], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]),
eval(parse(text = "LETTERS210729[met]"))]),
y = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_2], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
}
}
}
Expand All @@ -65,7 +70,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
else {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
unique(Data$Group)[C], unique(Data$Group)[H],
"T_test", sep = "_")))
}
Expand All @@ -82,14 +87,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
else {
for (met in 1:(ncol(Data) - 2)) {
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
"U_test", sep = "_"), wilcox.test(x = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_1], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]),
eval(parse(text = "LETTERS210729[met]"))]),
y = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_2], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
}
}
}
Expand All @@ -102,7 +107,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
else {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
unique(Data$Group)[C], unique(Data$Group)[H],
"U_test", sep = "_")))
}
Expand Down Expand Up @@ -143,7 +148,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
print("###########################################")
}
rm(list = setdiff(ls(), c("Data_renamed", "Data",
"Result", "LETTERS37232", "event",
"Result", "LETTERS210729", "event",
"P_hoc", "Colors", "significant_variable_only")))
print("statistical test has finished")
Result_T <- Result[, 1]
Expand Down Expand Up @@ -176,14 +181,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
else {
for (met in 1:(ncol(Data) - 2)) {
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
"T_test", sep = "_"), t.test(x = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_1], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]),
eval(parse(text = "LETTERS210729[met]"))]),
y = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_2], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
}
}
}
Expand All @@ -196,7 +201,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
else {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
unique(Data$Group)[C], unique(Data$Group)[H],
"T_test", sep = "_")))
}
Expand All @@ -213,14 +218,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
else {
for (met in 1:(ncol(Data) - 2)) {
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
unique(Data$Group)[Gnum_1], unique(Data$Group)[Gnum_2],
"U_test", sep = "_"), wilcox.test(x = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_1], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]),
eval(parse(text = "LETTERS210729[met]"))]),
y = (eval(parse(text = paste("Data",
unique(Data$Group)[Gnum_2], sep = "_")))[,
eval(parse(text = "LETTERS37232[met]"))]))[["p.value"]])
eval(parse(text = "LETTERS210729[met]"))]))[["p.value"]])
}
}
}
Expand All @@ -233,7 +238,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
else {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
unique(Data$Group)[C], unique(Data$Group)[H],
"U_test", sep = "_")))
}
Expand All @@ -244,14 +249,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
print("U-test has finished")
for (met in 1:(ncol(Data) - 2)) {
Ano_In <- aov(eval(parse(text = LETTERS37232[met])) ~
Ano_In <- aov(eval(parse(text = LETTERS210729[met])) ~
Group, data = Data_final)
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
"Anova", sep = "_"), summary(Ano_In)[[1]][["Pr(>F)"]][1])
}
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
"Anova", sep = "_")))
}
Rounder <- Rounder + 1
Expand All @@ -260,15 +265,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
print("Anova went wrong")
}
for (met in 1:(ncol(Data) - 2)) {
assign(paste(LETTERS37232[met], "Anova_Post_Hoc",
sep = "_"), DescTools::PostHocTest(aov(eval(parse(text = LETTERS37232[met])) ~
assign(paste(LETTERS210729[met], "Anova_Post_Hoc",
sep = "_"), DescTools::PostHocTest(aov(eval(parse(text = LETTERS210729[met])) ~
Group, data = Data_final), method = "scheffe"))
}
for (Ano_numb in 1:nrow(eval(parse(text = paste(LETTERS37232[met],
for (Ano_numb in 1:nrow(eval(parse(text = paste(LETTERS210729[met],
"Anova_Post_Hoc", sep = "_")))[["Group"]])) {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
"Anova_Post_Hoc", sep = "_")))[["Group"]][Ano_numb,
4]
}
Expand All @@ -280,14 +285,14 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
print("Anova & PostHoc has finished")
for (met in 1:(ncol(Data) - 2)) {
Kru_In <- kruskal.test(eval(parse(text = LETTERS37232[met])) ~
Kru_In <- kruskal.test(eval(parse(text = LETTERS210729[met])) ~
Group, data = Data_final)
assign(paste(as.character(LETTERS37232[met]),
assign(paste(as.character(LETTERS210729[met]),
"Kruskal_Wallis", sep = "_"), Kru_In[["p.value"]])
}
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
"Kruskal_Wallis", sep = "_")))
}
Rounder <- Rounder + 1
Expand All @@ -296,15 +301,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
print("Kruskal went wrong")
}
for (met in 1:(ncol(Data) - 2)) {
assign(paste(LETTERS37232[met], "Dunn_Post_Hoc",
sep = "_"), FSA::dunnTest(eval(parse(text = LETTERS37232[met])) ~
assign(paste(LETTERS210729[met], "Dunn_Post_Hoc",
sep = "_"), FSA::dunnTest(eval(parse(text = LETTERS210729[met])) ~
Group, data = Data_final, method = "bh"))
}
for (Kru_numb in 1:length(eval(parse(text = paste(LETTERS37232[met],
for (Kru_numb in 1:length(eval(parse(text = paste(LETTERS210729[met],
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])) {
if (is.na(Result[1, Rounder]) == T) {
for (met_1 in 1:(ncol(Data_final) - 2)) {
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS37232[met_1],
Result[met_1, Rounder] <- eval(parse(text = paste(LETTERS210729[met_1],
"Dunn_Post_Hoc", sep = "_")))[["res"]][["P.adj"]][Kru_numb]
}
Rounder <- Rounder + 1
Expand All @@ -327,15 +332,15 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
}
}
AN_Post_names <- NULL
for (nrow in 1:nrow(eval(parse(text = paste(LETTERS37232[met],
for (nrow in 1:nrow(eval(parse(text = paste(LETTERS210729[met],
"Anova_Post_Hoc", sep = "_")))[["Group"]])) {
AN_Post_names <- rbind(AN_Post_names, rownames(eval(parse(text = paste(LETTERS37232[met],
AN_Post_names <- rbind(AN_Post_names, rownames(eval(parse(text = paste(LETTERS210729[met],
"Anova_Post_Hoc", sep = "_")))[["Group"]])[nrow])
}
DU_post_names <- NULL
for (nrow in 1:length(eval(parse(text = paste(LETTERS37232[met],
for (nrow in 1:length(eval(parse(text = paste(LETTERS210729[met],
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])) {
DU_post_names <- rbind(DU_post_names, (eval(parse(text = paste(LETTERS37232[met],
DU_post_names <- rbind(DU_post_names, (eval(parse(text = paste(LETTERS210729[met],
"Dunn_Post_Hoc", sep = "_")))[["res"]][["Comparison"]])[nrow])
}
rownames(Result) <- colnames(Data)[3:(ncol(Data_final))]
Expand All @@ -360,7 +365,7 @@ Allstats<-function (Data, Adjust_p_value = T, Adjust_method = "BH")
print("###########################################")
}
rm(list = setdiff(ls(), c("Data_renamed", "Data",
"Result", "LETTERS37232", "event",
"Result", "LETTERS210729", "event",
"P_hoc", "Colors", "significant_variable_only")))
print("statistical test has finished")
})
Expand Down

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