[英]Getting estimate and p-value into dataframe
我對R相當陌生。我的數據看起來像這樣(僅包含9000列和66行)
Time <- c(0, 6.4, 8.6, 15.2, 19.4, 28.1, 42.6, 73, 73, 85, 88, 88, 88, 88, 88)
ID1 <- c(55030, 54539, 54937, 48897, 58160, 54686, 55393, 47191, 39805, 37601, 51328, 28882, 45587, 60061, 31892, 28670)
ID2 <- c(20485, 11907, 10571, 20974, 10462, 11149, 20970, NA, NA, 9295, NA, 8714, 24446, 10748, 9037, 11859)
ID3 <- c(93914, 44482, 43705, 51144, 49485, 43908, 44324, 37342, 18872, 39660,61673, 43837, 36528, 44738, 41648, 11100)
DF <- data.frame (Time, ID1, ID2, ID3)
我想要一個看起來像這樣的數據框:
ID1,Rho,p值
ID2,Rho,p值
...
rho和p值是帶有時間和每個ID的cor.test(長矛手)的結果
我嘗試過的其他方法之一:
results <- data.frame(ID="", Estimate="", P.value="")
estimates = numeric(16)
pvalues = numeric(16)
for (i in 2:4){
test <- cor.test(DF[,1], DF[,i])
estimates[i] = test$estimate
pvalues[i] = test$p.value
}
R給了我以下錯誤:
Error: object 'test' not found
我也嘗試過:
result <- do.call(rbind,lapply(2:4, function(x) {
cor.result<-cor.test(DF[,1],DF[,x])
pvalue <- cor.result$p.value
estimate <- cor.result$estimate
return(data.frame(pvalue = pvalue, estimate = estimate))
})
)
R給了我一個類似的錯誤
Error: object 'cor.result' not found
我敢肯定這是一個簡單的解決方法,但似乎無法解決。 任何幫助都超過了歡迎。
這是我跑步后得到的
dput(head(SmallDataset[,1:5]))
structure(list(Species = c("Human.hsapiens", "Chimpanzee.ptroglodytes",
"Gorilla.ggorilla", "Orangutan.pabelii", "Gibbon.nleucogenys",
"Macaque.mmulatta"), Time = c(0, 6.4, 8.61, 15.2, 19.43, 28.1
), ID1 = c(55030, 54539, 54937, 48897, 58160, 54686), ID2 = c(20485,
11907, 10571, 20974, 10462, 11149), ID3 = c(93914, 44482, 43705,
51144, 49485, 43908)), row.names = c(NA, -6L), class = c("tbl_df",
"tbl", "data.frame"))
我的解決方案涉及在lapply調用中定義一個函數
##
library(dplyr)
###Create dataframe
Time <- c(0, 6.4, 8.6, 15.2, 19.4, 28.1, 42.6, 73, 73, 85, 88, 88, 88, 88, 88, 89)
ID1 <- c(55030, 54539, 54937, 48897, 58160, 54686, 55393, 47191, 39805, 37601, 51328, 28882, 45587, 60061, 31892, 28670)
ID2 <- c(20485, 11907, 10571, 20974, 10462, 11149, 20970, NA, NA, 9295, NA, 8714, 24446, 10748, 9037, 11859)
ID3 <- c(93914, 44482, 43705, 51144, 49485, 43908, 44324, 37342, 18872, 39660,61673, 43837, 36528, 44738, 41648, 11100)
DF <- data.frame (Time, ID1, ID2, ID3)
##Run the correlations
l2 <- lapply(2:4, function(i)cor.test(DF$Time, DF[,i]))
##Define function to extract p_value and coefficients
l3 <- lapply(l2, function(i){
return(tibble(estimate = i$estimate,
p_value = i$p.value))
})
##Create a dataframe with information
l4 <- bind_rows(l3) %>% mutate(ID = paste0("ID", 1:3)) ##Data frame with info
l4
考慮構建一個不那么lapply
的數據幀列表(一個迭代函數類似於for
但是建立一個長度相等的對象列表作為輸入)。 然后,將所有數據框元素行綁定在一起:
results <- lapply(2:4, function(i){
test <- cor.test(DF[,1], DF[,i])
data.frame(ID = names(DF)[i],
estimate = unname(test$estimate),
pvalues = unname(test$p.value))
})
final_df <- do.call(rbind, results)
final_df
# ID estimate pvalues
# 1 ID1 -0.6238591 0.009805341
# 2 ID2 -0.2270515 0.455676037
# 3 ID3 -0.4964092 0.050481533
注意:您為時間發布的數據缺少觀察值,因此無法立即與其他向量一起轉換為data.frame()
。 為了解決這個問題,我在結尾處補充了第六名88:
Time <- c(0, 6.4, 8.6, 15.2, 19.4, 28.1, 42.6, 73, 73, 85, 88, 88, 88, 88, 88, 88)
使用發布的SmallDataset:
SmallDataset <- structure(...)
results <- lapply(3:5, function(i){
test <- cor.test(SmallDataset$Time, SmallDataset[,i])
data.frame(ID = names(SmallDataset)[i],
estimate = unname(test$estimate),
pvalues = unname(test$p.value))
})
final_df <- do.call(rbind, results)
final_df
# ID estimate pvalues
# 1 ID1 0.03251407 0.9512461
# 2 ID2 -0.41733336 0.4103428
# 3 ID3 -0.60732484 0.2010166
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