導(dǎo)入所需要的包

library(xcms)

1.單個(gè)樣本

導(dǎo)入

data_raw <- readMSData("neg_20211-fa-68.mzML", mode = "onDisk",centroided = FALSE)

提取基峰色譜圖

bpis <- chromatogram(data_raw, aggregationFun = "max")
plot(bpis)

image.png

2.多組數(shù)據(jù)

導(dǎo)入

myfiles <- list.files(pattern = "^neg")
myfiles
pd <- data.frame(sample_name = sub(basename(myfiles), pattern = ".mzML",replacement = "", 
                                   fixed = TRUE),sample_group = c(rep("FA", 4), rep("HFD", 4)),stringsAsFactors = FALSE)
pd
data_raw <- readMSData(files = myfiles, pdata = new("NAnnotatedDataFrame", pd),mode = "onDisk")

提取基峰色譜圖

bpis <- chromatogram(data_raw, aggregationFun = "max")
#定義兩組顏色
group_colors <- c("blue","red")
names(group_colors) <- c("FA","HFD")
## 繪制所有色譜圖
plot(bpis, col = group_colors[data_raw$sample_group])

BPC.png

參考資料：

LCMS data preprocessing and analysis with xcms (bioconductor.org)