From ff55acb8cb544d475478894e9f67bc8563bf6cf7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Sun, 23 Jun 2019 22:23:03 +0200
Subject: [PATCH] Add RMB_EIC_prescreen_df
* R/mix.R(RMB_EIC_prescreen_df): New function. Instead of pdf file
with plots, this one records the data.frames to laters serve as
inputs to plotting stages.
---
R/mix.R | 101 ++++++++++++++++++++++++++++++---
man/RMB_EIC_prescreen_df.Rd | 29 ++++++++++
man/RMB_EIC_prescreen_intrn.Rd | 2 +-
3 files changed, 123 insertions(+), 9 deletions(-)
create mode 100644 man/RMB_EIC_prescreen_df.Rd
diff --git a/R/mix.R b/R/mix.R
index e2ede63..3d64763 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -314,7 +314,7 @@ v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="ar
##' @param cmpd_list ...
##' @param ppm_limit_fine ...
##' @param EIC_limit ...
-##' @author Emma Schymanski
+##' @author Emma Schymanski, Todor Kondić
RMB_EIC_prescreen_intrn <- function (archive_name, RMB_mode, FileList, cmpd_list,
ppm_limit_fine = 10, EIC_limit = 0.001) {
pdf_title <- paste(archive_name, "_EICscan.pdf", sep = "")
@@ -377,6 +377,91 @@ RMB_EIC_prescreen_intrn <- function (archive_name, RMB_mode, FileList, cmpd_list
+##' Prescreens. Writes data out. Adapted from ReSOLUTION
+##'
+##'
+##' @title Prescreen
+##' @param wd Absolute path to the directory that will contain the
+##' resulting data frame.
+##' @param RMB_mode ...
+##' @param FileList ...
+##' @param cmpd_list ...
+##' @param ppm_limit_fine ...
+##' @param EIC_limit ...
+##' @author Emma Schymanski, Todor Kondić
+RMB_EIC_prescreen_df <- function (wd, RMB_mode, FileList, cmpd_list,
+ ppm_limit_fine = 10, EIC_limit = 0.001) {
+
+
+ n_spec <- 0
+ cmpd_RT_maxI <- ""
+ msms_found <- ""
+ rts <- 0
+ max_I_prec <- ""
+ cmpd_RT_maxI_min <- ""
+ file_list <- read.csv(FileList, stringsAsFactors = FALSE)
+ cmpd_info <- read.csv(cmpd_list, stringsAsFactors = FALSE)
+ ncmpd <- nrow(cmpd_info)
+ odir=file.path(wd,"prescreen")
+ no_drama_mkdir(odir)
+ get_width <- function(maxid) {log10(maxid)+1}
+ id_field_width <- get_width(ncmpd)
+
+ fn_out<- function(id,suff) {file.path(odir,paste(formatC(id,width=id_field_width,flag=0),suff,".csv",sep=''))}
+ f <- mzR::openMSfile(file_list$Files[1])
+ for (i in 1:length(file_list$ID)) {
+ cpdID <- file_list$ID[i]
+ n_spec <- n_spec + 1
+ smiles <- tryCatch(RMassBank::findSmiles(cpdID), error = function(e) NA)
+ if (!is.na(smiles)) {
+ mz <- as.numeric(RMassBank::findMz(cpdID, RMB_mode)[3])
+ }
+ else {
+ mz <- as.numeric(RMassBank::findMz(cpdID, RMB_mode, retrieval = "unknown")[3])
+ }
+ eic <- RMassBank::findEIC(f, mz, limit = EIC_limit)
+ msms_found[n_spec] <- FALSE
+ msms <- RMassBank::findMsMsHR.mass(f, mz, 0.5, RMassBank::ppm(mz, ppm_limit_fine,
+ p = TRUE))
+ max_I_prec_index <- which.max(eic$intensity)
+ cmpd_RT_maxI[n_spec] <- eic[max_I_prec_index, 1]
+ max_I_prec[n_spec] <- eic[max_I_prec_index, 2]
+ cmpd_RT_maxI_min[n_spec] <- as.numeric(cmpd_RT_maxI[n_spec])/60
+ ## plot.new()
+ ## plot.window(range(eic$rt), range(eic$intensity))
+ ## box()
+ ## lines(eic$intensity ~ eic$rt)
+ write.csv(x=eic[c("rt","intensity")],file=fn_out(cpdID,".eic"),row.names=F)
+ for (specs in msms) {
+ if (specs@found == TRUE) {
+
+ df <- do.call(rbind, lapply(specs@children, function(sp) c(sp@rt,
+ intensity = max(sp@intensity))))
+ names(df) <- c("rt","intensity")
+ write.csv(x=df,file=fn_out(cpdID,".kids"),row.names=F)
+ ## lines(intensity ~ retentionTime, data = df, type = "h",
+ ## col = "blue")
+ msms_found[n_spec] <- TRUE
+ }
+ }
+ ## title(main = cpdID, xlab = "RT (sec)", ylab = "Intensity")
+ ## text(as.numeric(cmpd_RT_maxI[n_spec]), as.numeric(max_I_prec[n_spec]),
+ ## labels = as.numeric(cmpd_RT_maxI_min[n_spec]), pos = 4)
+ ## axis(1)
+ ## axis(2)
+ ## gc()
+ rts[i] <- (cmpd_RT_maxI[n_spec])
+ }
+ # dev.off()
+ write.csv(cbind(file_list$ID, cmpd_info$mz, cmpd_info$Name,
+ cmpd_RT_maxI, cmpd_RT_maxI_min, max_I_prec, msms_found),
+ file = file.path(odir,"RTs_wI.csv"),
+ row.names = F)
+}
+
+
+
+
@@ -396,6 +481,7 @@ RMB_EIC_prescreen_intrn <- function (archive_name, RMB_mode, FileList, cmpd_list
##' @author Todor Kondić
##' @export
presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EIC_limit=0.001,nm_arch="archive") {
+ wd <- normalizePath(wd)
gen_stgs_and_load(fn_data,stgs_alist,wd)
## Generate and load the compound list.
@@ -406,13 +492,12 @@ presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EI
## Generate file table.
fn_table <- gen_file_table(fn_data,n_cmpd,wd)
- curd <- setwd(wd)
- res <-RMB_EIC_prescreen_intrn(archive_name=nm_arch,RMB_mode=mode,
- FileList=fn_table,
- cmpd_list=fn_comp,
- ppm_limit_fine=ppm_lim_fine,
- EIC_limit=EIC_limit)
- setwd(curd)
+ #curd <- setwd(wd)
+ res <-RMB_EIC_prescreen_df(wd=wd,RMB_mode=mode, FileList=fn_table,
+ cmpd_list=fn_comp,
+ ppm_limit_fine=ppm_lim_fine,
+ EIC_limit=EIC_limit)
+ #setwd(curd)
res
}
diff --git a/man/RMB_EIC_prescreen_df.Rd b/man/RMB_EIC_prescreen_df.Rd
new file mode 100644
index 0000000..13016b1
--- /dev/null
+++ b/man/RMB_EIC_prescreen_df.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{RMB_EIC_prescreen_df}
+\alias{RMB_EIC_prescreen_df}
+\title{Prescreen}
+\usage{
+RMB_EIC_prescreen_df(wd, RMB_mode, FileList, cmpd_list,
+ ppm_limit_fine = 10, EIC_limit = 0.001)
+}
+\arguments{
+\item{wd}{Absolute path to the directory that will contain the
+resulting data frame.}
+
+\item{RMB_mode}{...}
+
+\item{FileList}{...}
+
+\item{cmpd_list}{...}
+
+\item{ppm_limit_fine}{...}
+
+\item{EIC_limit}{...}
+}
+\description{
+Prescreens. Writes data out. Adapted from ReSOLUTION
+}
+\author{
+Emma Schymanski, Todor Kondić
+}
diff --git a/man/RMB_EIC_prescreen_intrn.Rd b/man/RMB_EIC_prescreen_intrn.Rd
index 2374aac..ef62fcf 100644
--- a/man/RMB_EIC_prescreen_intrn.Rd
+++ b/man/RMB_EIC_prescreen_intrn.Rd
@@ -24,5 +24,5 @@ RMB_EIC_prescreen_intrn(archive_name, RMB_mode, FileList, cmpd_list,
Prescreens. Ripped off from ReSOLUTION
}
\author{
-Emma Schymanski
+Emma Schymanski, Todor Kondić
}
--
GitLab