how to convert lmd file to csv? [Flow Cytometry data]
lmd file extension is often used for generating flow cytometry data. But this couldn’t be directly used for processing either in R or Python. Is there a way to somehow convert it to csv or some renowned format?
This is a bit tricky. So far I haven’t come across any such direct conversion function. Perhaps, fcs is a more common format for flow-cytometry. Hence, we will first need to convert lmd to fcs and then to csv format.
Step 1: lmd to fcs [Using R]
# install source("http://bioconductor.org/biocLite.R") biocLite("flowCore") # convert library(tools) # for file_path_sans_ext if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = '3.10') BiocManager::install("flowCore") library(flowCore) in.fname <- 'Filename.LMD' folder <- '/home/User/Desktop/Data/' x <- read.FCS(paste0(folder, in.fname)) summary(x) out.fname <- paste0(file_path_sans_ext(in.fname), '.fcs') write.FCS(x, paste0(folder, out.fname))
Note: Change User and Filename with your desired path and filename respectively
Your fcs file will be saved in the same folder.
Step 2: fcs to csv
This could be done simply using the read.FCS() function to read in a FCS file, and then using write.delim() or write.csv() to create a .txt or .csv file.
Answered By – Sachin Motwani