导入所需要的包
library(xcms)
1.单个样本
导入
data_raw <- readMSData("neg_20211-fa-68.mzML", mode = "onDisk",centroided = FALSE)
提取基峰色谱图
bpis <- chromatogram(data_raw, aggregationFun = "max")
plot(bpis)
image.png
2.多组数据
导入
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")
提取基峰色谱图
bpis <- chromatogram(data_raw, aggregationFun = "max")
#定义两组颜色
group_colors <- c("blue","red")
names(group_colors) <- c("FA","HFD")
## 绘制所有色谱图
plot(bpis, col = group_colors[data_raw$sample_group])
BPC.png
参考资料:
LCMS data preprocessing and analysis with xcms (bioconductor.org)