From 9bcf7c6cc168079aec1db8651bcc98c9e0c4f327 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 1 Jul 2019 05:54:47 +0200
Subject: [PATCH] Streamline mix.R and run.R
More sensible (re)loading of the configuration files, encapsulation of
certain operations and other fixes
* mix.R(get_.*): Generate various filenames.
* mix.R(various intermediate wrappers around RMassBank calls):
removed.
* run.R(presc.do): Adjust to changes in mix.R
* man: Update docs.
* NAMESPACE: Update exports.
---
NAMESPACE | 3 -
R/mix.R | 89 ++----------------------
R/run.R | 24 +++++--
man/{gen_comp_list.Rd => gen_cmpd_l.Rd} | 6 +-
man/gen_cmpdl_and_load.Rd | 6 +-
man/{gen_file_table.Rd => gen_ftable.Rd} | 10 +--
man/gen_stgs_and_load.Rd | 4 +-
man/mb.do.Rd | 4 +-
man/mb.prep.Rd | 6 +-
man/mb.prep.single.Rd | 25 -------
man/mb.prep.v.Rd | 25 -------
man/mb.single.Rd | 25 -------
man/no_drama_mkdir.Rd | 2 +-
man/p.sw.Rd | 45 ------------
man/presc.do.Rd | 8 ++-
man/presc.p.Rd | 31 ---------
man/presc.single.Rd | 34 ---------
man/presc.v.Rd | 28 --------
man/sw.do.Rd | 7 +-
man/sw.single.1.Rd | 35 ----------
man/sw.single.Rd | 40 -----------
man/sw.single.next.Rd | 29 --------
man/v.Rd | 40 -----------
23 files changed, 50 insertions(+), 476 deletions(-)
rename man/{gen_comp_list.Rd => gen_cmpd_l.Rd} (90%)
rename man/{gen_file_table.Rd => gen_ftable.Rd} (82%)
delete mode 100644 man/mb.prep.single.Rd
delete mode 100644 man/mb.prep.v.Rd
delete mode 100644 man/mb.single.Rd
delete mode 100644 man/p.sw.Rd
delete mode 100644 man/presc.p.Rd
delete mode 100644 man/presc.single.Rd
delete mode 100644 man/presc.v.Rd
delete mode 100644 man/sw.single.1.Rd
delete mode 100644 man/sw.single.Rd
delete mode 100644 man/sw.single.next.Rd
delete mode 100644 man/v.Rd
diff --git a/NAMESPACE b/NAMESPACE
index 0f870cc..2c3e0d5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,8 +3,5 @@
export(mb.do)
export(mb.prep)
export(presc.do)
-export(presc.p)
export(presc.plot)
-export(presc.single)
-export(presc.v)
export(sw.do)
diff --git a/R/mix.R b/R/mix.R
index fc46261..135c39d 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -70,6 +70,9 @@ fn_data2wd <- function(fn_data,dest) {
},vectorize.args="fn_data")
f(fn_data)
}
+
+get_presc_d <- function(wd) { file.path(wd,"prescreen")}
+gen_presc_d <- function(wd) { no_drama_mkdir(get_presc_d(wd))}
@@ -86,7 +89,7 @@ get_stgs_fn <- function(wd) {
}
get_ftable_fn <- function(wd) {
- f <- function(wd) file.path(wd,"ftable.ini")
+ f <- function(wd) file.path(wd,"ftable.csv")
fv <- Vectorize(f,vectorize.args=c("wd"))
fv(wd)
}
@@ -229,61 +232,6 @@ reconf <- function(wd) {## Load the settings.
RMassBank::loadList(fn_cmpd_l)
}
-##' 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)
- gen_stgs_and_load(stgs_alist,wd)
-
- ## Generate and load the compound list.
- x <- gen_cmpdl_and_load(wd,fn_cmpd_l)
- fn_cmpd_l <- 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_cmpd_l,
- ppm_limit_fine=ppm_lim_fine,
- EIC_limit=EIC_limit)
- #setwd(curd)
- 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)
-}
-
##' Prescreens. Writes data out. Adapted from ReSOLUTION
##'
##'
@@ -367,33 +315,6 @@ RMB_EIC_prescreen_df <- function (wd, RMB_mode, FileList, cmpd_list,
row.names = F)
}
-
-
-##' Parallel version of presc.single.
-##'
-##' @title Parallel version of presc.single
-##' @param cl Cluster object.
-##' @param fn_data Sequence of mzML files.
-##' @param fn_cmpd_l Filename of the compound list.
-##' @param mode RMB mode.
-##' @param ppm_lim_fine See ReSOLUTION.
-##' @param EIC_limit See ReSOLUTION.
-##' @return Nothing useful.
-##' @author Todor Kondić
-##' @export
-presc.p<-function(cl,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 <- function(fn_data,stgs_alist,wd) presc.single(fn_data=fn_data,stgs_alist=stgs_alist,wd=wd,mode=mode,
- fn_cmpd_l=fn_cmpd_l,ppm_lim_fine=ppm_lim_fine,EIC_limit=EIC_limit)
-
- parallel::clusterMap(cl,fun=f,fn_data,stgs_alist,wd)
-
-}
-
-
##' Plot the output of prescreen.
##'
##' @title Plot the Output of Prescreen
@@ -414,7 +335,7 @@ presc.plot <- function(wd,out="prescreen.pdf",pal="Dark2",cex=0.75,digits=6) {
for (i in seq(length(eics))) {
eic <- eics[[i]]
maybekid <- maybekids[[i]]
- fn_ini <- lapply(wd,function(x) file.path(x,list.files(path=x,patt="*.ini")[[1]]))
+ fn_ini <- lapply(wd,get_stgs_fn)
lbls <- lapply(fn_ini,function(x) {s <- yaml::yaml.load_file(x);s$spectraList[[1]]$ce})
plot.new()
diff --git a/R/run.R b/R/run.R
index 66389a1..9e95cd4 100644
--- a/R/run.R
+++ b/R/run.R
@@ -13,20 +13,34 @@ attch<-function(...) paste(...,sep='')
##' @title Prescreening on bunch of files.
##' @param fn_data The mzML files. Basis for the out directory name
##' generation.
-##' @param fn_cmpd_list The compound list CSV.
+##' @param fn_cmpd_l The compound list.
##' @param mode RMB mode.
+##' @param dest Destination directory.
##' @param proc Amount of processors, or FALSE.
+##' @param fn_cmpd_list The compound list CSV.
##' @return Nothing useful.
##' @author Todor Kondić
##' @export
-presc.do<-function(fn_data,fn_cmpd_list,mode,proc=F) {
+presc.do<-function(fn_data,fn_cmpd_l,mode,dest=".",proc=F,...) {
+ conf(fn_data,fn_cmpd_l,dest)
+ fread <- function(fn_data) {
+ wd <- fn_data2wd(fn_data,dest)
+ gen_presc_d(wd)
+ reconf(wd)
+ message("Currently processing: ",wd)
+ fn_ftable <- get_ftable_fn(wd)
+ fn_cmpd_l <- get_cmpd_l_fn(wd)
+ RMB_EIC_prescreen_df(wd=wd,RMB_mode=mode,FileList=fn_ftable,
+ cmpd_list=fn_cmpd_l,...)
+ }
if (proc) {
- cl<-parallel::makeCluster(proc,type='FORK')
- presc.p(cl=cl,fn_data,fn_cmpd_l=fn_cmpd_list,mode=mode)
+ cl<-parallel::makeCluster(proc)
+ parallel::clusterEvalQ(cl,library(rmbmix))
+ parallel::clusterMap(cl,fread,fn_data)
} else {
- presc.v(fn_data,fn_cmpd_l=fn_cmpd_list,mode)
+ lapply(fn_data,fread)
}
}
diff --git a/man/gen_comp_list.Rd b/man/gen_cmpd_l.Rd
similarity index 90%
rename from man/gen_comp_list.Rd
rename to man/gen_cmpd_l.Rd
index e242bbf..e2a69af 100644
--- a/man/gen_comp_list.Rd
+++ b/man/gen_cmpd_l.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mix.R
-\name{gen_comp_list}
-\alias{gen_comp_list}
+\name{gen_cmpd_l}
+\alias{gen_cmpd_l}
\title{Generate Compound List File}
\usage{
-gen_comp_list(src_fn, dest_fn)
+gen_cmpd_l(src_fn, dest_fn)
}
\arguments{
\item{src_fn}{The input compound list CSV filename.}
diff --git a/man/gen_cmpdl_and_load.Rd b/man/gen_cmpdl_and_load.Rd
index eb28d78..a782c7b 100644
--- a/man/gen_cmpdl_and_load.Rd
+++ b/man/gen_cmpdl_and_load.Rd
@@ -4,12 +4,12 @@
\alias{gen_cmpdl_and_load}
\title{Generate and Load the RMassBank Compound List}
\usage{
-gen_cmpdl_and_load(fn_data, wd, fn_cmpdl)
+gen_cmpdl_and_load(wd, fn_cmpdl)
}
\arguments{
-\item{fn_data}{The mzML filename.}
-
\item{wd}{Directory under which results are archived.}
+
+\item{fn_cmpdl}{The input compound list filename.}
}
\value{
Named list. The key \code{fn_cmpdl} is the path of the
diff --git a/man/gen_file_table.Rd b/man/gen_ftable.Rd
similarity index 82%
rename from man/gen_file_table.Rd
rename to man/gen_ftable.Rd
index c7daf7f..de5f27d 100644
--- a/man/gen_file_table.Rd
+++ b/man/gen_ftable.Rd
@@ -1,17 +1,17 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mix.R
-\name{gen_file_table}
-\alias{gen_file_table}
+\name{gen_ftable}
+\alias{gen_ftable}
\title{Generate and Load the RMassBank Settings File}
\usage{
-gen_file_table(fn_data, n_cmpd, wd)
+gen_ftable(fn_data, wd, n_cmpd)
}
\arguments{
\item{fn_data}{The mzML filename.}
-\item{n_cmpd}{Number of compounds.}
-
\item{wd}{Directory under which results are archived.}
+
+\item{n_cmpd}{Number of compounds.}
}
\value{
File path of the file table.
diff --git a/man/gen_stgs_and_load.Rd b/man/gen_stgs_and_load.Rd
index 53ee0bb..1fb26fc 100644
--- a/man/gen_stgs_and_load.Rd
+++ b/man/gen_stgs_and_load.Rd
@@ -4,11 +4,9 @@
\alias{gen_stgs_and_load}
\title{Generate and Load the RMassBank Settings File}
\usage{
-gen_stgs_and_load(fn_data, stgs, wd)
+gen_stgs_and_load(stgs, wd)
}
\arguments{
-\item{fn_data}{The mzML filename.}
-
\item{stgs}{Settings named list, or a settings filename.}
\item{wd}{Directory under which results are archived.}
diff --git a/man/mb.do.Rd b/man/mb.do.Rd
index 73e319d..d77aec2 100644
--- a/man/mb.do.Rd
+++ b/man/mb.do.Rd
@@ -4,13 +4,11 @@
\alias{mb.do}
\title{Perform the Mass Bank workflow}
\usage{
-mb.do(mb, rdir = ".", proc = F)
+mb.do(mb, proc = F)
}
\arguments{
\item{mb}{The list of prepared mbWorkspace objects.}
-\item{rdir}{Root data dir.}
-
\item{proc}{Split work between this amount of processes. If FALSE
(or, 1), run sequential.}
}
diff --git a/man/mb.prep.Rd b/man/mb.prep.Rd
index 43fdac8..2463441 100644
--- a/man/mb.prep.Rd
+++ b/man/mb.prep.Rd
@@ -4,14 +4,10 @@
\alias{mb.prep}
\title{Prepare mbWorkspace objects}
\usage{
-mb.prep(w, rdir = ".")
+mb.prep(w)
}
\arguments{
\item{w}{A list of spectral workspace inputs.}
-
-\item{rdir}{Data root.}
-
-\item{proc}{Split work between this amount of processes. If FALSE}
}
\value{
Named list of prepared mbWorkspace objects.
diff --git a/man/mb.prep.single.Rd b/man/mb.prep.single.Rd
deleted file mode 100644
index e0f116c..0000000
--- a/man/mb.prep.single.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.prep.single}
-\alias{mb.prep.single}
-\title{Prepare Single mbWorkspace object}
-\usage{
-mb.prep.single(w, fn_info, fn_stgs)
-}
-\arguments{
-\item{w}{MsmsWorkspace object.}
-
-\item{fn_info}{Filename of the infolist to be generated.}
-
-\item{fn_stgs}{Filename of the RMassBank settings.}
-}
-\value{
-A mbWorkspace object.
-}
-\description{
-Prepare single mbWorkspace object based on the workspace, the
-infolist name and RMassBank settings.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/mb.prep.v.Rd b/man/mb.prep.v.Rd
deleted file mode 100644
index 2aba41e..0000000
--- a/man/mb.prep.v.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.prep.v}
-\alias{mb.prep.v}
-\title{Vectorized mb.prep function.}
-\usage{
-mb.prep.v(w, fn_info, fn_stgs)
-}
-\arguments{
-\item{w}{A sequence of msmsWorkspaces.}
-
-\item{fn_info}{A sequence of infolist filenams to be generated.}
-
-\item{fn_stgs}{A sequence of settings associated with each
-msmsWorkspace object.}
-}
-\value{
-A list of mbWorkspaces.
-}
-\description{
-Vectorize mb.prep function.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/mb.single.Rd b/man/mb.single.Rd
deleted file mode 100644
index 107e606..0000000
--- a/man/mb.single.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mb.single}
-\alias{mb.single}
-\title{Single MassBank workflow.}
-\usage{
-mb.single(mb, infodir, fn_stgs)
-}
-\arguments{
-\item{mb}{A mbWorkspace object.}
-
-\item{infodir}{Directory containing the infolist.}
-
-\item{fn_stgs}{The settings associated with the mbWorkspace
-object.}
-}
-\value{
-A mbWorkflow object.
-}
-\description{
-Performs a single MassBank workflow after preparation.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/no_drama_mkdir.Rd b/man/no_drama_mkdir.Rd
index aa1bc12..c33d17d 100644
--- a/man/no_drama_mkdir.Rd
+++ b/man/no_drama_mkdir.Rd
@@ -7,7 +7,7 @@
no_drama_mkdir(path)
}
\arguments{
-\item{path}{Name of the directory.}
+\item{path}{Names of the directories.}
}
\value{
The character string containing the input argument \code{path}.
diff --git a/man/p.sw.Rd b/man/p.sw.Rd
deleted file mode 100644
index def4a60..0000000
--- a/man/p.sw.Rd
+++ /dev/null
@@ -1,45 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{p.sw}
-\alias{p.sw}
-\title{Parallel Spectral Workflow.}
-\usage{
-p.sw(cl, fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
- archdir = "archive", lastStep = 8, combine = F,
- combdest = "combined")
-}
-\arguments{
-\item{cl}{Cluster.}
-
-\item{fn_data}{A sequence of mzML input files.}
-
-\item{stgs_alist}{A list of named list of settings, or a list of
-filenames of YAML files containing the settings.}
-
-\item{wd}{The list of working directories.}
-
-\item{fn_cmpd_list}{The compound list characterising the mixtures.}
-
-\item{mode}{Same as in msmsRead.}
-
-\item{readMethod}{Same as in msmsRead.}
-
-\item{archdir}{Name of the archive.}
-
-\item{lastStep}{The last step in spectral workflow.}
-
-\item{combine}{If TRUE, use combineMultiplicies to merge
-workspaces corresponding to different collisional energies.}
-
-\item{combdest}{Combine destination directory.}
-}
-\value{
-A named list of spectral workspaces. The names are derived
-from data filenames.
-}
-\description{
-Interface to parallel spectral workflow.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/presc.do.Rd b/man/presc.do.Rd
index f001b9b..162677c 100644
--- a/man/presc.do.Rd
+++ b/man/presc.do.Rd
@@ -4,17 +4,21 @@
\alias{presc.do}
\title{Prescreening on bunch of files.}
\usage{
-presc.do(fn_data, fn_cmpd_list, mode, proc = F)
+presc.do(fn_data, fn_cmpd_l, mode, dest = ".", proc = F, ...)
}
\arguments{
\item{fn_data}{The mzML files. Basis for the out directory name
generation.}
-\item{fn_cmpd_list}{The compound list CSV.}
+\item{fn_cmpd_l}{The compound list.}
\item{mode}{RMB mode.}
+\item{dest}{Destination directory.}
+
\item{proc}{Amount of processors, or FALSE.}
+
+\item{fn_cmpd_list}{The compound list CSV.}
}
\value{
Nothing useful.
diff --git a/man/presc.p.Rd b/man/presc.p.Rd
deleted file mode 100644
index 3df93cb..0000000
--- a/man/presc.p.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.p}
-\alias{presc.p}
-\title{Parallel version of presc.single}
-\usage{
-presc.p(cl, fn_data, fn_cmpd_l, mode, ppm_lim_fine = 10,
- EIC_limit = 0.001)
-}
-\arguments{
-\item{cl}{Cluster object.}
-
-\item{fn_data}{Sequence of mzML files.}
-
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{mode}{RMB mode.}
-
-\item{ppm_lim_fine}{See ReSOLUTION.}
-
-\item{EIC_limit}{See ReSOLUTION.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Parallel version of presc.single.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/presc.single.Rd b/man/presc.single.Rd
deleted file mode 100644
index 4263e02..0000000
--- a/man/presc.single.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.single}
-\alias{presc.single}
-\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)
-}
-\arguments{
-\item{fn_data}{The mzML filename.}
-
-\item{stgs_alist}{Settings named list, or a settings filename.}
-
-\item{wd}{Directory under which results are archived.}
-
-\item{mode}{RMB mode.}
-
-\item{fn_cmpd_l}{Filename of the compound list.}
-
-\item{ppm_lim_fine}{The ppm_limit_fine argument to RMB_EIC_Prescreen}
-
-\item{EIC_limit}{Passed down to RMB_EIC_Prescreen.}
-}
-\value{
-result of RMB_EIC_Prescreen
-}
-\description{
-Wrapper for a single prescreening call. Produces output in the
-usual mix method places.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/presc.v.Rd b/man/presc.v.Rd
deleted file mode 100644
index 2728a2e..0000000
--- a/man/presc.v.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% 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
-}
diff --git a/man/sw.do.Rd b/man/sw.do.Rd
index 21ad74f..51ff104 100644
--- a/man/sw.do.Rd
+++ b/man/sw.do.Rd
@@ -4,12 +4,13 @@
\alias{sw.do}
\title{Perform MassBank Workflow on Multiple Compound Mixtures}
\usage{
-sw.do(fn_data, fn_cmpd_list, mode, dest = ".", combine = F, proc = F)
+sw.do(fn_data, fn_cmpd_l, mode, dest = ".", combine = F, proc = F,
+ split = 3)
}
\arguments{
\item{fn_data}{List of mzML data filenames to be processed.}
-\item{fn_cmpd_list}{Compound list.}
+\item{fn_cmpd_l}{Compound list.}
\item{mode}{as in msmsRead.}
@@ -20,6 +21,8 @@ workspaces corresponding to different collisional energies.}
\item{proc}{Split work between this amount of processes. If FALSE
(or, 1), run sequential.}
+
+\item{split}{This is the last step before combine}
}
\value{
A named list of msmsWorkspace objects.
diff --git a/man/sw.single.1.Rd b/man/sw.single.1.Rd
deleted file mode 100644
index 725cf14..0000000
--- a/man/sw.single.1.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single.1}
-\alias{sw.single.1}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture (step 1)}
-\usage{
-sw.single.1(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
- readMethod = "mzR")
-}
-\arguments{
-\item{fn_data}{A mzML data file.}
-
-\item{stgs_alist}{RMassBank settings. It can either be a named
-list of settings, or a filename of a YAML file.}
-
-\item{wd}{The name of the work directory.}
-
-\item{fn_cmpd_list}{The file name of he compound list
-corresponding to \code{fn_data}.}
-
-\item{mode}{Modes as described in the standard workflow vignette
-of RMassBank.}
-
-\item{readMethod}{Default read method is "mzR". Consult the
-documentation of \code{msmsRead} for details.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs the first step of the compound mixture workflow on a single mzML file.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/sw.single.Rd b/man/sw.single.Rd
deleted file mode 100644
index ba0b18f..0000000
--- a/man/sw.single.Rd
+++ /dev/null
@@ -1,40 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single}
-\alias{sw.single}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture}
-\usage{
-sw.single(fn_data, stgs_alist, wd, fn_cmpd_list, mode,
- readMethod = "mzR", archdir = "archive", lastStep = 8)
-}
-\arguments{
-\item{fn_data}{A mzML data file.}
-
-\item{stgs_alist}{RMassBank settings. It can either be a named
-list of settings, or a filename of a YAML file.}
-
-\item{wd}{The name of the work directory.}
-
-\item{fn_cmpd_list}{The file name of he compound list
-corresponding to \code{fn_data}.}
-
-\item{mode}{Modes as described in the standard workflow vignette
-of RMassBank.}
-
-\item{readMethod}{Default read method is "mzR". Consult the
-documentation of \code{msmsRead} for details.}
-
-\item{archdir}{The directory to store R objects created during
-workflow execution.}
-
-\item{lastStep}{The last step in the workflow. Default is eight.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs a compound mixture workflow on a single mzML file.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/sw.single.next.Rd b/man/sw.single.next.Rd
deleted file mode 100644
index 78baeab..0000000
--- a/man/sw.single.next.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{sw.single.next}
-\alias{sw.single.next}
-\title{RMassBank Spectral Workflow on a Single Compound Mixture (after step 1)}
-\usage{
-sw.single.next(w, wd, archdir = "archive", lastStep = 8)
-}
-\arguments{
-\item{w}{The msmsWorkspace object that was processed by
-sw.single.1.}
-
-\item{wd}{The current working dir.}
-
-\item{archdir}{The directory to store R objects created during
-workflow execution.}
-
-\item{lastStep}{The last step in the workflow. Default is eight.}
-}
-\value{
-MsmsWorkspace object.
-}
-\description{
-Runs steps after sw.single.1 of compound mixture workflow on a
-single mzML file.
-}
-\author{
-Todor Kondić
-}
diff --git a/man/v.Rd b/man/v.Rd
deleted file mode 100644
index 8038344..0000000
--- a/man/v.Rd
+++ /dev/null
@@ -1,40 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{v}
-\alias{v}
-\title{Vectorised Spectral Workflow.}
-\usage{
-v(fn_data, stgs_alist, wd, fn_cmpd_list, mode, readMethod = "mzR",
- archdir = "archive", lastStep = 8, combine = F)
-}
-\arguments{
-\item{fn_data}{A sequence of mzML input files.}
-
-\item{stgs_alist}{A list of named list of settings, or a list of
-filenames of YAML files containing the settings.}
-
-\item{wd}{The list of working directories.}
-
-\item{fn_cmpd_list}{The compound list characterising the mixtures.}
-
-\item{mode}{Same as in msmsRead.}
-
-\item{readMethod}{Same as in msmsRead.}
-
-\item{archdir}{Name of the archive.}
-
-\item{lastStep}{The last step of the spectral workflow.}
-
-\item{combine}{If TRUE, use combineMultiplicies to merge
-workspaces corresponding to different collisional energies.}
-}
-\value{
-A named list of spectral workspaces. The names are derived
-from data filenames.
-}
-\description{
-Interface to vectorised spectral workflow.
-}
-\author{
-Todor Kondić
-}
--
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