From 1826e6de83be6bed364d43697fb0e4c0ee5762ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Sun, 23 Jun 2019 23:18:58 +0200
Subject: [PATCH] Add presc.v
* R/mix.R(presc.v): New function. Vectorises presc.single.
* NAMESPACE: Update exports.
* man(presc.single.Rd,presc.v.Rd): Update docs.
---
NAMESPACE | 1 +
R/mix.R | 90 ++++++++++++++++++++++++++-------------------
man/presc.single.Rd | 4 +-
man/presc.v.Rd | 28 ++++++++++++++
4 files changed, 83 insertions(+), 40 deletions(-)
create mode 100644 man/presc.v.Rd
diff --git a/NAMESPACE b/NAMESPACE
index dee537f..7f850e6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,4 +3,5 @@
export(mb.do)
export(mb.prep)
export(presc.single)
+export(presc.v)
export(sw.do)
diff --git a/R/mix.R b/R/mix.R
index 3d64763..3124d8d 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -146,7 +146,42 @@ gen_file_table <- function(fn_data,n_cmpd,wd) {
fn_table
}
+##' Wrapper for a single prescreening call. Produces output in the
+##' usual mix method places.
+##'
+##' @title Wrapper for RMB_EIC_Prescreen
+##' @param fn_data The mzML filename.
+##' @param stgs_alist Settings named list, or a settings filename.
+##' @param wd Directory under which results are archived.
+##' @param mode RMB mode.
+##' @param fn_cmpd_l Filename of the compound list.
+##' @param ppm_lim_fine The ppm_limit_fine argument to RMB_EIC_Prescreen
+##' @param EIC_limit Passed down to RMB_EIC_Prescreen.
+##' @return result of RMB_EIC_Prescreen
+##' @author Todor Kondić
+##' @export
+presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EIC_limit=0.001) {
+ no_drama_mkdir(wd)
+ wd <- normalizePath(wd)
+ gen_stgs_and_load(fn_data,stgs_alist,wd)
+
+ ## Generate and load the compound list.
+ x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_l)
+ fn_comp <- x$fn_cmpdl
+ n_cmpd <- x$n
+
+ ## Generate file table.
+ fn_table <- gen_file_table(fn_data,n_cmpd,wd)
+
+ #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
+}
##' Runs a compound mixture workflow on a single mzML file.
##'
@@ -252,8 +287,24 @@ mb.single<-function(mb,infodir,fn_stgs) {
res
}
-
-
+##' Vectorises presc.single.
+##'
+##' @title Vectorises presc.single
+##' @param fn_data Sequence of mzML filenames.
+##' @param fn_cmpd_l Compound list filename.
+##' @param mode RMB mode.
+##' @param ppm_lim_fine Prescreen fine limit (see ReSOLUTION prescreening function).
+##' @param EIC_limit Prescreen EIC limit (see ReSOLUTION prescreening function).
+##' @return Nothing useful.
+##' @author Todor Kondić
+##' @export
+presc.v<-function(fn_data,fn_cmpd_l,mode,ppm_lim_fine=10,EIC_limit=0.001) {
+ idir<-function(n) file.path(".",stripext(n))
+ wd <- sapply(fn_data,idir)
+ stgs_alist <- sapply(wd,function(d) {paste(d,".ini",sep='')})
+ f<-Vectorize(presc.single,vectorize.args=c("fn_data","stgs_alist","wd"),SIMPLIFY=F)
+ f(fn_data,stgs_alist,wd,mode=mode,fn_cmpd_l=fn_cmpd_l,ppm_lim_fine=ppm_lim_fine,EIC_limit=EIC_limit)
+}
##' Interface to vectorised spectral workflow.
@@ -465,42 +516,7 @@ RMB_EIC_prescreen_df <- function (wd, RMB_mode, FileList, cmpd_list,
-##' Wrapper for a single prescreening call. Produces output in the
-##' usual mix method places.
-##'
-##' @title Wrapper for RMB_EIC_Prescreen
-##' @param fn_data The mzML filename.
-##' @param stgs_alist Settings named list, or a settings filename.
-##' @param wd Directory under which results are archived.
-##' @param mode RMB mode.
-##' @param fn_cmpd_l Filename of the compound list.
-##' @param ppm_lim_fine The ppm_limit_fine argument to RMB_EIC_Prescreen
-##' @param EIC_limit Passed down to RMB_EIC_Prescreen.
-##' @param nm_arch Archive prefix.
-##' @return result of RMB_EIC_Prescreen
-##' @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.
- x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_l)
- fn_comp <- x$fn_cmpdl
- n_cmpd <- x$n
-
- ## Generate file table.
- fn_table <- gen_file_table(fn_data,n_cmpd,wd)
-
- #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/presc.single.Rd b/man/presc.single.Rd
index b2f14dd..4263e02 100644
--- a/man/presc.single.Rd
+++ b/man/presc.single.Rd
@@ -5,7 +5,7 @@
\title{Wrapper for RMB_EIC_Prescreen}
\usage{
presc.single(fn_data, stgs_alist, wd, mode, fn_cmpd_l, ppm_lim_fine = 10,
- EIC_limit = 0.001, nm_arch = "archive")
+ EIC_limit = 0.001)
}
\arguments{
\item{fn_data}{The mzML filename.}
@@ -21,8 +21,6 @@ presc.single(fn_data, stgs_alist, wd, mode, fn_cmpd_l, ppm_lim_fine = 10,
\item{ppm_lim_fine}{The ppm_limit_fine argument to RMB_EIC_Prescreen}
\item{EIC_limit}{Passed down to RMB_EIC_Prescreen.}
-
-\item{nm_arch}{Archive prefix.}
}
\value{
result of RMB_EIC_Prescreen
diff --git a/man/presc.v.Rd b/man/presc.v.Rd
new file mode 100644
index 0000000..2728a2e
--- /dev/null
+++ b/man/presc.v.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mix.R
+\name{presc.v}
+\alias{presc.v}
+\title{Vectorises presc.single}
+\usage{
+presc.v(fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10, EIC_limit = 0.001)
+}
+\arguments{
+\item{fn_data}{Sequence of mzML filenames.}
+
+\item{fn_cmpd_l}{Compound list filename.}
+
+\item{mode}{RMB mode.}
+
+\item{ppm_lim_fine}{Prescreen fine limit (see ReSOLUTION prescreening function).}
+
+\item{EIC_limit}{Prescreen EIC limit (see ReSOLUTION prescreening function).}
+}
+\value{
+Nothing useful.
+}
+\description{
+Vectorises presc.single.
+}
+\author{
+Todor Kondić
+}
--
GitLab