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Martin Loos authored and cran-robot committed Jul 23, 2014
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18 changes: 7 additions & 11 deletions DESCRIPTION
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Expand Up @@ -3,18 +3,14 @@ Type: Package
Title: Detecting, combining and filtering isotope, adduct and homologue
series relations in high-resolution mass spectrometry (HRMS)
data
Version: 1.2
Date: 2012-10-15
Version: 1.3
Date: 2014-07-23
Author: Martin Loos
Maintainer: Martin Loos <Martin.Loos@eawag.ch>
Description: Screening a HRMS data set for peaks related by (1) isotope
patterns, (2) different adducts of the same molecule and/or (3)
homologue series. The resulting isotopic pattern and adduct
groups can then be combined to so-called components, with
homologue series information attached. Also allows plotting and
filtering HRMS data for mass defects, frequent m/z distances
and components vs. non-components.
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
License: GPL-2
Packaged: 2012-10-18 09:06:40 UTC; loosmart
Depends: enviPat(>= 1.7), nontargetData(>= 1.1), mgcv(>= 1.7-22)
Packaged: 2014-07-23 10:40:11 UTC; uchemadmin
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2012-10-18 18:11:44
Date/Publication: 2014-07-23 13:15:40
61 changes: 31 additions & 30 deletions MD5
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@@ -1,45 +1,46 @@
70cfe11b07025ff86b550a19e4e5bd2a *DESCRIPTION
df390c53434517b304ac5db487184641 *NAMESPACE
c6bcfb9808f58e711d2fc603fed6cbc2 *R/adduct.search.R
4b581855f0337ef51a8d983cb03f4604 *DESCRIPTION
b3e3ed15978dd61558086d6842cf1a23 *NAMESPACE
a33d0fabd405d186553ed6d8760a6038 *NEWS
776df5ea4ac41b8b1a72f9d9aa65eae8 *R/adduct.search.R
80b9c2f147a4d9cef81491c1b9d95d25 *R/combine.R
2053804fc57a6fdb694416d680c5bb95 *R/deter.iso.R
41405f255745478ca4662fe774ac68d1 *R/homol.search.R
ec8797996668be63d3a0ecfe701100ab *R/make.isos.R
cff0eb3c38d9beb31b7c1e474a94baf0 *R/homol.search.R
f3d6c963d9ad4e432bc21682e0a212d1 *R/make.isos.R
e9ac33bbec7b0ca7443f65e1bb4bddbd *R/ms.filter.R
dce6444dc8fd5cbbe466df7632e24466 *R/nontarget-internal.R
683c241820eec5ce926ffa27d5dcaa2f *R/nontarget.R
c3697e5e9d73666db084adbe03080d1c *R/pattern.search.R
7dce7b1cd09d25bae22c5e1d389e0fc5 *R/nontarget.R
2e1ff48684adc67837a05e9ea705b0f8 *R/pattern.search.R
ae4632d4bc7d2efd6bb192f2e8c5bed1 *R/pattern.search2.R
d58307aa7a623d10412b51fb5fd6d48d *R/plotadduct.R
94e2bf21892c52a1dc329995e852eeb5 *R/plotall.R
faca91d002c38892c60e9132a3cbe349 *R/plotcomp.R
384b902494f176e0c2a6446679cf7b5e *R/plotdefect.R
c3842b0e1161ff48c0e6b4d2b7b2eef3 *R/plotdefect.R
ad1c6ab0d4736672fca83ff8722eded0 *R/plotdiff.R
015326b4fb3fda5e7eb1d18254e40c42 *R/plotgroup.R
25f4f6d55fb82be99910b05e111a9b8b *R/plothomol.R
17178087618d84df22f43e14d9020b6e *R/plotgroup.R
56ae814c20986784a8e5ced14e584053 *R/plothomol.R
01bdb350695c3f910be559128accf021 *R/plotisotopes.R
aea23e170739fce51498cf0b53f3c707 *R/rm.sat.R
f7f31b70e62c8967b83b8c28ed760ca2 *data/adduct_list.rda
181d9ec48728e569c9b3692ca5bcca57 *data/iso_list.rda
e6f1efb5ed75468cc251f234d2b663a1 *data/peaklist.rda
ef490821f3aec95909a5c6ef7616ebb8 *man/adduct.search.Rd
52e6e905c3e6d811f87a5ce8e3e2c97d *man/adduct_list.Rd
be2f4fe791c1d1f241c195aed02e2eb0 *man/combine.Rd
e9e7afc1bc2b2cf3cdbfa6e94ea3c144 *man/deter.iso.Rd
fc2490de1e0f997fcec81e7bbecdabf2 *man/homol.search.Rd
8370c4f2a5f451313eec8bec238fd91a *man/iso_list.Rd
b7e423b815e5feee1c0735d4a7a259c0 *man/make.isos.Rd
e59139a02e75467c10c14eb3b4118555 *man/ms.filter.Rd
7ee636f3ed4d32eff5361863d80d7379 *man/nontarget-package.Rd
921308307d868203fa1c803b44e37377 *man/pattern.search.Rd
e973c2f1adaf26bc5a742809a04b6ede *man/adduct.search.Rd
f22c96186ea98fe0eb25be65269dbb97 *man/combine.Rd
88e8e4f0a8c97681ad947349f7d684e0 *man/deter.iso.Rd
352c56ddca5c875775e84cbe9a86afea *man/homol.search.Rd
e7232f60d6e2f7325653ad7980f15f15 *man/make.isos.Rd
1dcbe4bbafdce4960e57c1d87647089c *man/ms.filter.Rd
b68b7b152f39b2e6a4d182867b86ecd6 *man/nontarget-package.Rd
3908a96bc7952343af381cb70a0975d0 *man/pattern.search.Rd
9d3e0cbc2bf80f28cf40c5083889c10f *man/pattern.search2.Rd
98afa2cfbc0238d2fc169c16f7288f81 *man/peaklist.Rd
e1008b7237691b69e5d11034e2883f3f *man/plotadduct.Rd
7d7547f0028451045db1143b07ceb503 *man/plotall.Rd
db80295da663f0570824baad81f5c229 *man/plotcomp.Rd
0b51997f72774d7028f231dfc70a3fa7 *man/plotdefect.Rd
5003f21330f0409ed9c9b870213748cc *man/plotdiff.Rd
59de92488ced0ac8dd52920250910560 *man/plotgroup.Rd
6803ec3c28ec363cb8031f33677220fb *man/plothomol.Rd
3706d5485ff21072e82360b49cac144d *man/plotdefect.Rd
d901b5237252096dc1fbd3a2e4f38408 *man/plotdiff.Rd
0595e639c597ca8cf33869d80833ec8c *man/plotgroup.Rd
b139c1ffd8a08c61b750faececce91f4 *man/plothomol.Rd
bc3f4eff3a70a155d144a38e0054b385 *man/plotisotopes.Rd
9e5ecb95fef23842f9fbced149ff9354 *man/rm.sat.Rd
7c88148ffd26c3aae6db0fb071410960 *src/adductCpp.cpp
d36e4f6e765c9f6905730995141d01a4 *src/massCpp.cpp
4d0ac0448b61ca0ee8b5d1868befb46a *man/rm.sat.Rd
dc7a5173afbaaf36888f2f4ce17fdadb *src/adductCpp.cpp
0438bad0fc74c7a44b815690433ae25e *src/homologues.cpp
35b326b0393ca3bb794c07c68b263086 *src/massCpp.cpp
6c112f852affd92c0d3801dca797538f *src/quantization.cpp
ef0b6a860b904cd6f3e9816c50965d55 *src/searchTree.cpp
6 changes: 5 additions & 1 deletion NAMESPACE
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@@ -1 +1,5 @@
exportPattern("^[[:alpha:]]+")
exportPattern(adduct.search,combine,make.isos,deter.iso,homol.search,ms.filter,nontarget,pattern.search,pattern.search2,plotadduct,plotall,plotcomp,plotdefect,plotdiff,plotgroup,plothomol,plotisotopes,rm.sat)
useDynLib(nontarget,adduct,mass,homol_1,metagroup,peak_search,boxtree,kdtree4,search_boxtree,search_kdtree)
importFrom("enviPat")
importFrom("nontargetData")
importFrom("mgcv")
7 changes: 7 additions & 0 deletions NEWS
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@@ -0,0 +1,7 @@
nontarget News

CHANGES in version 1.3:

(1) src, R, man - several bugs debugged
(2) R - pattern.search2 introduced
(3) R - homol.search upgraded
192 changes: 117 additions & 75 deletions R/adduct.search.R
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@@ -1,17 +1,22 @@
adduct.search <-
function(
peaklist,adduct_list,
rttol=0,mztol=2,massfrac=0.1,ppm=TRUE,
adducts=c("M+H","M+K","M+Na"),ion_mode="positive",
peaklist,
adducts,
rttol=0,
mztol=2,
massfrac=0.1,
ppm=TRUE,
use_adducts=c("M+H","M+K","M+Na"),
ion_mode="positive",
entry=20
){
){

############################################################################
# (0) check inputs #########################################################
if(massfrac>1 || massfrac<=0){ stop("massfrac must be >0 and <=1") };
if( massfrac>1 || massfrac<=0 ){ stop("massfrac must be >0 and <=1") };
if(ion_mode!="positive" & ion_mode!="negative"){stop("ion mode: positive or negative?")}
for(i in 1:length(adducts)){if(any(adduct_list[,1]==adducts[i])!=TRUE & any(adduct_list[adduct_list[,1]==adducts[i],6]==ion_mode)){stop(paste("Adduct ",adducts[i]," not in adduct_list!",sep=""))}};
for(i in 1:length(adducts)){if((adduct_list[adduct_list[,1]==adducts[i],6]!=ion_mode)){stop(paste(adducts[i]," not in ion mode ",ion_mode,sep=""))}};
for(i in 1:length(use_adducts)){if(any(adducts[,1]==use_adducts[i])!=TRUE & any(adducts[adducts[,1]==use_adducts[i],6]==ion_mode)){stop(paste("Adduct ",use_adducts[i]," not in adducts!",sep=""))}};
for(i in 1:length(use_adducts)){if((adducts[adducts[,1]==use_adducts[i],6]!=ion_mode)){stop(paste(use_adducts[i]," not in ion mode ",ion_mode,sep=""))}};
if(length(peaklist)>3){stop("peaklist with > 3 columns not allowed")}
############################################################################
cat("\n (1) Assemble lists...");
Expand All @@ -25,29 +30,29 @@ function(
getit2<-rep("0",alls); # (2) from which peak?
getit4<-rep("0",alls); # (3) to which peak?
getit5<-rep("0",alls); # (4) within [1] large or [2] small mass tolerance?
# (1.3) retrieve selected subset of adduct_list
adducts<-as.character(levels(as.factor(adducts)))
these<-match(adducts,adduct_list[,1]);
# (1.3) retrieve selected subset of adducts
use_adducts<-as.character(levels(as.factor(use_adducts)))
these<-match(use_adducts,adducts[,1]);
these<-these[is.na(these)==FALSE];
add<-adduct_list[these,];
add<-adducts[these,];
add<-add[add[,6]==ion_mode,];
if(length(add[,1])<1){stop("No selected adducts in list!")};
if(length(add[,1])<1){stop("No selected use_adducts among adducts ... abort!")};
add2<-data.frame(0,0,0,0,0);
add3<-c();
names(add2)<-c("mult1","mass1","mult2","mass2","count")
that<-c(2);
for(i in 1:(length(add[,1]))){
for(j in 1:length(add[,1])){
if(i!=j){
add2<-rbind(add2,rep(0,5));
add2[that,1]<-add[i,4];
add2[that,2]<-add[i,5];
add2[that,3]<-add[j,4];
add2[that,4]<-add[j,5];
that<-c(that+1);
add3<-c(add3,paste(add[i,1],add[j,1],sep="<->"));
}
}; #j
for(j in 1:length(add[,1])){
if(i!=j){
add2<-rbind(add2,rep(0,5));
add2[that,1]<-add[i,4];
add2[that,2]<-add[i,5];
add2[that,3]<-add[j,4];
add2[that,4]<-add[j,5];
that<-c(that+1);
add3<-c(add3,paste(add[i,1],add[j,1],sep="<->"));
}
}; #j
}; #i
add2<-add2[-1,];
#data.frame(add3,add2);
Expand All @@ -63,46 +68,83 @@ function(
getit4a<-rep(0,alls*entry);
getit5a<-rep(0,alls*entry);
maxmass<-max(peaklist[,1]);
#dyn.load("C:\\Program Files\\R\\R-2.13.1\\bin\\i386\\adductCpp.dll");
#dyn.load(paste(.libPaths(),"/nontarget/temp/adductCpp.dll",sep=""));
result<-.C("adduct",
as.double(samples[,1]),as.double(samples[,3]),as.integer(length(samples[,1])), # 3
as.double(mztol*2),as.double(massfrac*2),as.double(rttol), # 6
as.integer(length(add2[,1])), # 7
as.double(add2[,1]),as.double(add2[,2]),as.double(add2[,3]),as.double(add2[,4]),as.integer(add2[,5]), # 12
as.integer(entry),as.integer(ppm2), # 14
as.integer(getit1a),as.integer(getit2a),as.integer(getit4a),as.integer(getit5a) # 18
,PACKAGE="nontarget"
as.double(samples[,1]),
as.double(samples[,3]),
as.integer(length(samples[,1])), # 3
as.double(mztol*2),
as.double(massfrac*2),
as.double(rttol), # 6
as.integer(length(add2[,1])), # 7
as.double(add2[,1]),
as.double(add2[,2]),
as.double(add2[,3]),
as.double(add2[,4]),
as.integer(add2[,5]), # 12
as.integer(entry),
as.integer(ppm2), # 14
as.integer(getit1a),
as.integer(getit2a),
as.integer(getit4a),
as.integer(getit5a), # 18
PACKAGE="nontarget"
);
# (1) which adduct?
for(i in 1:(alls-1)){for(j in 1:entry){if(result[15][[1]][(i-1)*entry+j]!=0){getit1[i]<-paste(getit1[i],result[15][[1]][(i-1)*entry+j],sep="/")}}};
for(i in 1:(alls-1)){
for(j in 1:entry){
if(result[15][[1]][(i-1)*entry+j]!=0){
getit1[i]<-paste(getit1[i],result[15][[1]][(i-1)*entry+j],sep="/")
}
}
};
# (2) from which peak?
for(i in 1:(alls-1)){for(j in 1:entry){if(result[16][[1]][(i-1)*entry+j]!=0){getit2[i]<-paste(getit2[i],result[16][[1]][(i-1)*entry+j],sep="/")}}};
for(i in 1:(alls-1)){
for(j in 1:entry){
if(result[16][[1]][(i-1)*entry+j]!=0){
getit2[i]<-paste(getit2[i],getback[result[16][[1]][(i-1)*entry+j]],sep="/")
}
}
};
# (3) to which peak?
for(i in 1:(alls-1)){for(j in 1:entry){if(result[17][[1]][(i-1)*entry+j]!=0){getit4[i]<-paste(getit4[i],result[17][[1]][(i-1)*entry+j],sep="/")}}};
for(i in 1:(alls-1)){
for(j in 1:entry){
if(result[17][[1]][(i-1)*entry+j]!=0){
getit4[i]<-paste(getit4[i],getback[result[17][[1]][(i-1)*entry+j]],sep="/")
}
}
};
# (4) tolerance: small or large?
for(i in 1:(alls-1)){for(j in 1:entry){
if(result[18][[1]][(i-1)*entry+j]==1){getit5[i]<-paste(getit5[i],"small",sep="/")};
if(result[18][[1]][(i-1)*entry+j]==2){getit5[i]<-paste(getit5[i],"large",sep="/")};
}};
if(result[13][[1]]!=entry){cat("WARNING: entry overflow -> links missing!")};
for(i in 1:(alls-1)){
for(j in 1:entry){
if(result[18][[1]][(i-1)*entry+j]==1){
getit5[i]<-paste(getit5[i],"small",sep="/")
};
if(result[18][[1]][(i-1)*entry+j]==2){
getit5[i]<-paste(getit5[i],"large",sep="/")
};
}
};
if(result[13][[1]]!=entry){
cat("WARNING: entry overflow -> links missing!")
};
#data.frame(ID,getit4,getit2,getit1,getit5)
rm(result);
#dyn.unload(paste(.libPaths(),"/nontarget/temp/adductCpp.dll",sep=""));
############################################################################

############################################################################
# correct outputs for missing adduct combis (only submatrix searched!)
# correct outputs for missing adduct combis (only submatrix searched!) #####
for(i in 1:alls){
if(getit1[i]!="none"){
this12<-as.numeric(strsplit(as.character(getit1[i]),"/")[[1]][-1]);
if(length(this12)==1){
getit1[i]<-paste("none//",add3[this12],"//",sep="");
}else{
getit1[i]<-paste("none//",add3[this12[1]],"//",sep="");
for(j in 2:length(this12)){getit1[i]<-paste(getit1[i],add3[this12[j]],"//",sep="");}
};
};
if(getit1[i]!="none"){
this12<-as.numeric(strsplit(as.character(getit1[i]),"/")[[1]][-1]);
if(length(this12)==1){
getit1[i]<-paste("none//",add3[this12],"//",sep="");
}else{
getit1[i]<-paste("none//",add3[this12[1]],"//",sep="");
for(j in 2:length(this12)){
getit1[i]<-paste(getit1[i],add3[this12[j]],"//",sep="");
}
};
};
};
for(i in 1:alls){
if(getit4[i]!="0"){
Expand All @@ -116,20 +158,20 @@ function(
for(j in 1:length(this2a)){
this2<-c(this2,strsplit(as.character(this2a[j]),"<->")[[1]][1]);
this3<-c(this3,strsplit(as.character(this2a[j]),"<->")[[1]][2]);
};
};
for(j in 1:length(this1)){
this10<-strsplit(as.character(getit4[as.numeric(this1[j])]),"/")[[1]]
this11<-strsplit(as.character(getit1[as.numeric(this1[j])]),"//")[[1]]
if((any(this10==as.character(i)) & any(this11==paste(this3[j],"<->",this2[j],sep=""))) == FALSE ){
getit4[as.numeric(this1[j])]<-paste(getit4[as.numeric(this1[j])],i,sep="/");
if(getit1[as.numeric(this1[j])]=="none"){
getit1[as.numeric(this1[j])]="none//"
getit1[as.numeric(this1[j])]<-paste(getit1[as.numeric(this1[j])],paste(this3[j],"<->",this2[j],"//",sep=""),sep="");
}else{
getit1[as.numeric(this1[j])]<-paste(getit1[as.numeric(this1[j])],paste(this3[j],"<->",this2[j],"//",sep=""),sep="");
}
getit5[as.numeric(this1[j])]<-paste(getit5[as.numeric(this1[j])],this5[j],sep="/");
};
this10<-strsplit(as.character(getit4[as.numeric(this1[j])]),"/")[[1]]
this11<-strsplit(as.character(getit1[as.numeric(this1[j])]),"//")[[1]]
if((any(this10==as.character(i)) & any(this11==paste(this3[j],"<->",this2[j],sep=""))) == FALSE ){
getit4[as.numeric(this1[j])]<-paste(getit4[as.numeric(this1[j])],i,sep="/");
if(getit1[as.numeric(this1[j])]=="none"){
getit1[as.numeric(this1[j])]="none//"
getit1[as.numeric(this1[j])]<-paste(getit1[as.numeric(this1[j])],paste(this3[j],"<->",this2[j],"//",sep=""),sep="");
}else{
getit1[as.numeric(this1[j])]<-paste(getit1[as.numeric(this1[j])],paste(this3[j],"<->",this2[j],"//",sep=""),sep="");
}
getit5[as.numeric(this1[j])]<-paste(getit5[as.numeric(this1[j])],this5[j],sep="/");
};
};
};
};
Expand All @@ -139,11 +181,11 @@ function(

############################################################################
# (4) group ################################################################
cat("\n (3) Group peaks...");
cat("\n (3) Group peaks ...");
############################################################################
group1<-c(); # groupnumber?
group2<-c(); # which peaks?
group3<-c(); # which adducts?
group3<-c(); # which use_adducts?
group4<-rep(0,alls); # groupnumber? 1-alls
groupnumber<-c(1);
getit1b<-getit1;
Expand All @@ -154,9 +196,9 @@ function(
this2a<-strsplit(as.character(getit1b[i]),"//")[[1]][-1];
this2<-c();this3<-c();
for(j in 1:length(this2a)){
this2<-c(this2,strsplit(as.character(this2a[j]),"<->")[[1]][1]);
this3<-c(this3,strsplit(as.character(this2a[j]),"<->")[[1]][2]);
};
this2<-c(this2,strsplit(as.character(this2a[j]),"<->")[[1]][1]);
this3<-c(this3,strsplit(as.character(this2a[j]),"<->")[[1]][2]);
};
this4<-levels(as.factor(this2));
for(j in 1:length(this4)){
# assemble group information ########################################
Expand Down Expand Up @@ -227,7 +269,7 @@ function(
};
############################################################################
# count hits !
hits<-data.frame(adducts,rep(0,length(adducts)));
hits<-data.frame(use_adducts,rep(0,length(use_adducts)));
names(hits)<-c("names","counts");
for(i in 1:length(group1)){
this1<-strsplit(as.character(group3[i]),"/")[[1]];
Expand All @@ -245,12 +287,12 @@ function(
group1[k]<-paste("/",group1[k],"/",sep="")
}
grouping<-data.frame(group1,group2,group3);
names(grouping)<-c("group ID","peak IDs","adducts");
names(grouping)<-c("group ID","peak IDs","use_adducts");
############################################################################
adducts<-data.frame(samples[,1:3],ID,group4,getit4,getit1,getit5);
names(adducts)<-c(names(samples)[1:3],"peak ID","group ID","to ID","adduct(s)","mass tolerance");
adduct<-list(adducts,parameters,grouping,hits,overlaps);
names(adduct)<-c("Adducts","Parameters","Peaks in adduct groups","Number of adducts","Number of peaks with grouped adducts overlapping");
list_adducts<-data.frame(peaklist[,1:3],ID,group4,getit4,getit1,getit5);
names(list_adducts)<-c(names(peaklist)[1:3],"peak ID","group ID","to ID","adduct(s)","mass tolerance");
adduct<-list(list_adducts,parameters,grouping,hits,overlaps);
names(adduct)<-c("adducts","Parameters","Peaks in adduct groups","Adduct counts","Number of peaks with grouped adducts overlapping");
cat("done.\n\n");
############################################################################

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