From 578de64f33181e8503aad5b7b65e871d6347e2bb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Sun, 23 Jun 2019 16:12:26 +0200
Subject: [PATCH] Fix presc.single
* R/mix.R(presc.single): Now loads the component list properly.
---
R/mix.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index 6b69747..e2ede63 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -86,7 +86,6 @@ gen_comp_list<-function(src_fn,dest_fn) {
## CAS
casvals<-if ("CASRN" %in% names(df)) df$CASRN else rep(NA,sz)
if (is.null(haha)) stop("Unable to read SMILES from the input compound list.")
-
outdf<-data.frame(ID=1:sz,Name=nms,SMILES=haha,CAS=casvals,RT=rep(NA,sz))
write.csv(outdf,file=dest_fn,row.names=F,na="")
length(nms)
@@ -125,6 +124,7 @@ gen_cmpdl_and_load <- function(fn_data,wd,fn_cmpdl) {
fn_data <- normalizePath(fn_data)
fn_comp<-file.path(wd,paste(basename(fn_data),".comp.csv",sep=''))
n_cmpd<-gen_comp_list(fn_cmpdl,fn_comp)
+ RMassBank::loadList(fn_comp)
list(fn_cmpdl=fn_comp,n=n_cmpd)
}
@@ -340,7 +340,7 @@ RMB_EIC_prescreen_intrn <- function (archive_name, RMB_mode, FileList, cmpd_list
}
eic <- RMassBank::findEIC(f, mz, limit = EIC_limit)
msms_found[n_spec] <- FALSE
- msms <- RMassBank::findMsMsHR.mass(f, mz, 0.5, ppm(mz, ppm_limit_fine,
+ msms <- RMassBank::findMsMsHR.mass(f, mz, 0.5, RMassBank::ppm(mz, ppm_limit_fine,
p = TRUE))
max_I_prec_index <- which.max(eic$intensity)
cmpd_RT_maxI[n_spec] <- eic[max_I_prec_index, 1]
--
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