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Update fct_groupCorr.R to incorporate rt correction #29

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Update fct_groupCorr.R to incorporate rt correction #29

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8 changes: 8 additions & 0 deletions R/fct_groupCorr.R
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Original file line number Diff line number Diff line change
Expand Up @@ -750,6 +750,7 @@ getMaxScans <- function(object){
if(nfiles == 1){
if (file.exists(filepaths(object@xcmsSet)[1])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
xraw@scantime <- object@xcmsSet@rt$corrected[[1]]
maxscans <- length(xraw@scantime)
}else {
stop('Raw data file:',filepaths(object@xcmsSet)[1],' not found ! \n');
Expand All @@ -759,6 +760,7 @@ getMaxScans <- function(object){
for (f in 1:nfiles){
if(file.exists(filepaths(object@xcmsSet)[f])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[f], profstep=0);
xraw@scantime <- object@xcmsSet@rt$corrected[[f]];
maxscans <- max(maxscans, length(xraw@scantime));
} else {
stop('Raw data file:',filepaths(object@xcmsSet)[f],' not found ! \n');
Expand Down Expand Up @@ -787,6 +789,7 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){
if (file.exists(filepaths(object@xcmsSet)[1])) {

xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
xraw@scantime <- object@xcmsSet@rt$corrected[[1]]
maxscans <- length(xraw@scantime)
scantimes[[1]] <- xraw@scantime
pdata <- as.data.frame(object@xcmsSet@peaks)
Expand All @@ -809,6 +812,7 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){

if (file.exists(filepaths(object@xcmsSet)[1])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
xraw@scantime <- object@xcmsSet@rt$corrected[[1]]
maxscans <- length(xraw@scantime)
} else {
stop('Raw data file:',filepaths(object@xcmsSet)[1],' not found ! \n');
Expand All @@ -832,6 +836,7 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){
if (file.exists(filepaths(object@xcmsSet)[f])) {
#read sample
xraw <- xcmsRaw(filepaths(object@xcmsSet)[f], profstep=0);
xraw@scantime <- object@xcmsSet@rt$corrected[[f]];
maxscans.tmp <- length(xraw@scantime);
scantimes[[f]] <- xraw@scantime
if(maxscans.tmp > maxscans){
Expand Down Expand Up @@ -972,6 +977,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
for (f in 1:nfiles){
# cat('Reading raw data file:',filepaths(xs)[f])
xraw <- xcmsRaw(filepaths(xs)[f],profstep=0)
xraw@scantime <- xs@rt$corrected[[f]]
# cat(',', length(xraw@scantime),'scans. \n')
maxscans <- max(maxscans,length(xraw@scantime))
scantimes[[f]] <- xraw@scantime
Expand All @@ -981,6 +987,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
if (file.exists(filepaths(xs)[f])) {
# cat('Reading raw data file:',filepaths(xs)[f],'\n')
xraw <- xcmsRaw(filepaths(xs)[f],profstep=0)
xraw@scantime <- xs@rt$corrected[[f]]
# cat('Generating EIC\'s .. \n')
idx.peaks <- which(index == f);
if(length(idx.peaks)>0){
Expand All @@ -998,6 +1005,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
if (file.exists(filepaths(xs)[1])) {
#cat('Reading raw data file:',filepaths(xs)[1],'\n')
xraw <- xcmsRaw(filepaths(xs)[1],profstep=0)
xraw@scantime <- xs@rt$corrected[[1]]
#cat('Generating EIC\'s .. \n')
maxscans <- length(xraw@scantime)
scantimes[[1]] <- xraw@scantime
Expand Down