在 R 中：循环多个输入文件并根据每个输入文件的名称保存结果文件

Question

我是 R 的初学者。 我需要您的帮助来自动对列表“分数”（约 50 个文件）中包含的所有文件进行这些分析，并获取（并保存）摘要 output，其结果对应于每个输入文件（要命名的摘要 output类似于每个输入文件）。

现在，使用我的代码（附加），我可以一次获得一个输入文件的结果。 例如，如果我考虑名为“scores”的列表的第二个元素：

    file.names <- dir(pattern ="*.my.files") ### set the pattern name of the input files
    scores<-list() ### create a variable (list) that will contain the input data 
    for (k in 1:length(file.names)){scores[[k]] <- read.table(file.names[k],h=T)}

    ### scores[[2]] is the second element of the list named "scores"
    f1<-function(threshold) { glm(pheno ~ threshold + PC1 + PC2 + PC3 + PC4 +PC5 +PC6 +PC7+ PC8 + PC9 + C1+C2+C3+C4+C5+C6+C7+C8+C9, family='binomial',data=scores[[2]]) }


    m1<-apply(scores[[2]][2:9],2,f1) ### scores[[2]] is the second element of the list named "scores", 
                                     ###    the columns from 2 to 9 corresponds to the scores at the different p thresholds
                                     ###    after the first comma --> MARGIN: a vector giving the subscripts which the function 
                                     ###    will be applied over. E.g., for a matrix 1 indicates rows, 2 indicates columns, 
                                     ###    c(1, 2) indicates rows and columns. Where X has named dimnames, it can be a character vector 
                                     ###    selecting dimension names.

    ### calculate OR and R2:
    out1<-do.call(rbind,lapply(m1,function(z)summary(z)$coefficients[2,]))
    out1<-data.frame(out1)
    out1$OR<-exp(out1$Estimate)
    out1$ci_l<-exp(out1$Estimate-(1.96 * out1$Std..Error))
    out1$ci_u<-exp(out1$Estimate+(1.96 * out1$Std..Error))

    write.table(out1, file="estimates.txt", quote=F, sep=" ", dec=".", na="NA", row.names=T, col.names=T)

    ### calculate nagelkerkeR2: 
    library(sizeMat)
    full.nagel.r2<-do.call(rbind,lapply(m1,function(z)nagelkerkeR2(z)))
    full.nagel.r2<-data.frame(full.nagel.r2)
    n1<-glm(as.factor(pheno) ~ PC1 + PC2 + PC3 + PC4 +PC5 +PC6 +PC7+ PC8 + PC9 + C1+C2+C3+C4+C5+C6+C7+C8+C9, family='binomial',data=scores[[2]]) # null model
    full.nagel.r2$prs.r2<-full.nagel.r2[,1] - nagelkerkeR2(n1)

    write.table(full.nagel.r2, file="variance.txt", quote=F, sep=" ", dec=".", na="NA", row.names=T, col.names=T)

我还想知道是否可以合并“estimate.txt”和“variance.txt”文件的结果，以便为名为“scores”的列表中的每个输入文件获取一个 output 文件。

提前谢谢了。

Answer 1

只需使用数据框输入概括您的流程，或构建数据框的命名列表并迭代不同.txt文件的名称。 下面显示了lapply如何处理您的迭代和数据处理需求：

library(sizeMat)
...

# BUILD NAMED LIST OF DATA FRAMES
file.names <- dir(pattern ="*.my.files")
scores <- setNames(lapply(file.names, read.table, header=TRUE),
                   gsub(".my.files", "", file.names))

# DEFINED FUNCTION RECEIVING DF NAME PARAM
proc_scores <- function(df_name) {
   df <- scores[[df_name]]

   models <- lapply(df, function(threshold) {
       glm(pheno ~ threshold + PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9 + C1+C2+C3+C4+C5+C6+C7+C8+C9, 
           family='binomial', data=df)
   })

   ### calculate OR and R2:
   coeff_mat <- do.call(rbind, lapply(models, function(z) summary(z)$coefficients[2,]))
   coeff_df <- transform(data.frame(coeff_mat), 
      OR = exp(Estimate),
      ci_l = exp(Estimate - (1.96 * Std..Error)),
      ci_u = exp(Estimate + (1.96 * Std..Error)),
      score = df_name
  )

   # SAVE OUTPUT WITH DATA FRAME NAME
   write.table(coeff_df, file=paste0("estimates_", df_name, "_.txt"), quote=FALSE, 
               sep=" ", dec=".", na="NA", row.names=TRUE, col.names=TRUE)


   ### calculate nagelkerkeR2
   null.model <- glm(as.factor(pheno) ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9 + C1+C2+C3+C4+C5+C6+C7+C8+C9, 
                     family='binomial', data=df)

   nagel_mat <- do.call(rbind, lapply(models, function(z) nagelkerkeR2(z)))
   nagel_df <- data.frame(nagel_mat)
   nagel_df$prs.r2 <- nagel_df[,1] - nagelkerkeR2(null.model)
   nagel_df$score <- df_name

   # SAVE OUTPUT WITH DATA FRAME NAME
   write.table(nagel_df, file=paste0("variance_", df_name,"_.txt"), quote=FALSE, 
               sep=" ", dec=".", na="NA", row.names=TRUE, col.names=TRUE)

   # RETURN LIST OF DATA FRAMES
   return(list(coeff=coeff_df, nagel=nagel_df))
}


# ITERATELY CALL FUNCTION
results <- lapply(names(scores), proc_scores)

由于进程将数据导出到.txt并在列表中返回相同的对象，因此您可以相应地访问它们：

results[[1]]$coeff
results[[2]]$coeff   
results[[3]]$coeff
...

results[[1]]$nagel
results[[2]]$nagel
results[[3]]$nagel
...

对于结果的主编译：

master_coeff <- do.call(rbind, lapply(results, "[[", "coeff"))

# SAVE OUTPUT
write.table(master_coeff, file="estimates.txt", quote=FALSE, sep=" ",
            dec=".", na="NA", row.names=TRUE, col.names=TRUE)


master_nagel <- do.call(rbind, lapply(results, "[[", "nagel"))

# SAVE OUTPUT
write.table(master_nagel, file="variance.txt", quote=FALSE, 
            sep=" ", dec=".", na="NA", row.names=TRUE, col.names=TRUE)