如何循化命令处理相同类型的文件

Question

#使用DeepPseudoMSI将质谱文件转化成伪MS图像，命令只能一个一个更改文件名，怎么能够循环命令，将所有mzXML后缀的文件都转化成图像
#

source("code/pseudoMS-image-converter/convert2imageR.R")

mz.range = c(70, 1000)
rt.range = c(50, 1000)
mz.pixel = 1024
rt.pixel = 1024
noise.threshold = 500
output.path = "."
threads = 4
mz.shift = FALSE
rt.shift = FALSE
int.shift = FALSE

setwd("demo_data/")
file.name <- "QCP11.mzXML"

system.time(
  convert2image(
    file.name = file.name,
    mz.range = mz.range,
    rt.range = rt.range,
    mz.pixel = mz.pixel,
    rt.pixel = rt.pixel,
    noise.threshold = noise.threshold,
    output.path = output.path,
    threads = threads,
    mz.shift = mz.shift,
    rt.shift = rt.shift,
    int.shift = int.shift
  )
)

Answer 1

source("code/pseudoMS-image-converter/convert2imageR.R")

mz.range = c(70, 1000)
rt.range = c(50, 1000)
mz.pixel = 1024
rt.pixel = 1024
noise.threshold = 500
output.path = "."
threads = 4
mz.shift = FALSE
rt.shift = FALSE
int.shift = FALSE

setwd("demo_data/")
file.names <- list.files(pattern = "\\.mzXML$")

for (file.name in file.names) {
  system.time(
    convert2image(
      file.name = file.name,
      mz.range = mz.range,
      rt.range = rt.range,
      mz.pixel = mz.pixel,
      rt.pixel = rt.pixel,
      noise.threshold = noise.threshold,
      output.path = output.path,
      threads = threads,
      mz.shift = mz.shift,
      rt.shift = rt.shift,
      int.shift = int.shift
    )
  )
}