batch |
Get the MIR and related information from the files |
cbmd |
Combine two data with similar retention time while different mass range |
dotpanno |
Perform MS/MS dot product annotation for mgf file |
findline |
find line of the regression model for GC-MS |
findlipid |
Find lipid class of metabolites base on referenced Kendrick mass defect |
findmet |
Screen metabolites by Mass Defect |
findohc |
Screen organohalogen compounds by retention time, mass defect analysis and isotope relationship modified by literature report. Also support compounds with [M] and [M+2] ratio cutoff. |
getarea |
Get the peak information from sampels for SCCPs detection |
getareastd |
Get the peak information from SCCPs standards |
getbgremove |
Get the peak list with blank samples' peaks removed |
getbiotechrep |
Get the report for biological replicates. |
getcsv |
Convert an list object to csv file. |
getdata |
Get xcmsset object in one step with optimized methods. |
getdata2 |
Get XCMSnExp object in one step from structured folder path for xcms 3. |
getdoe |
Generate the group level rsd and average intensity based on DoE, |
getdwtus |
Density weighted intensity for one sample |
getfeaturesanova |
Get the features from anova, with p value, q value, rsd and power restriction |
getfeaturest |
Get the features from t test, with p value, q value, rsd and power restriction |
getfilter |
Filter the data based on row and column index |
getformula |
Get chemical formula for mass to charge ratio. |
getgrouprep |
Get the report for samples with biological and technique replicates in different groups |
getimputation |
Impute the peaks list data |
GetIntegration |
GetIntegration was mainly used for get the intergration of certain ion's chromatogram data and plot the data |
Getisotopologues |
Get the selected isotopologues at certain MS data |
getmass |
Get the exact mass of the isotopologues from a chemical formula or reaction's isotope patterns with the highest abundances |
getmassdefect |
Get mass defect with certain scaled factor |
getmd |
Import data and return the annotated matrix for GC/LC-MS by m/z range and retention time |
getmdh |
Get the high order unit based Mass Defect |
getmdr |
Get the raw Mass Defect |
getmr |
Get the mzrt profile and group information for batch correction and plot as a list directly from path with default setting |
getMSP |
read in MSP file as list for ms/ms or ms(EI) annotation |
getmzrt |
Get the mzrt profile and group information as a mzrt list and/or save them as csv or rds for further analysis. |
getmzrt2 |
Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object |
getmzrtcsv |
Covert the peaks list csv file into list |
getoverlapmass |
Get the overlap peaks by mass range |
getoverlappeak |
Get the overlap peaks by mass and retention time range |
getoverlaprt |
Get the overlap peaks by retention time |
getpower |
Get the index with power restriction for certain study with BH adjusted p-value and certain power. |
getpqsi |
Compute pooled QC linear index according to run order |
getQCraw |
get the data of QC compound for a group of data |
getrangecsv |
Get a mzrt list and/or save mz and rt range as csv file. |
getrmd |
Get the Relative Mass Defect |
getsccp |
Quantitative analysis for short-chain chlorinated paraffins(SCCPs) |
getsim |
output the similarity of two dataset |
gettechrep |
Get the report for technique replicates. |
gettimegrouprep |
Get the time series or two factor DoE report for samples with biological and technique replicates in different groups |
getupload |
Get the csv files from xcmsset/XCMSnExp/list object |
getupload2 |
Get the csv files to be submitted to Metaboanalyst |
getupload3 |
Get the csv files to be submitted to Metaboanalyst |
gifmr |
plot scatter plot for rt-mz profile and output gif file for mutiple groups |
Integration |
Just intergrate data according to fixed rt and fixed noise area |
list |
Demo data |
ma |
filter data by average moving box |
Mode |
define the Mode function |
plotanno |
Show MS/MS pmd annotation result |
plotcc |
plot the calibration curve with error bar, r squared and equation. |
plotden |
plot the density for multiple samples |
plotdwtus |
plot density weighted intensity for multiple samples |
plote |
plot EIC and boxplot for all peaks and return diffreport |
plotgroup |
Plot the response group of GC-MS |
plothist |
plot the density of the GC-MS data with EM algorithm to seperate the data into two log normal distribution. |
plothm |
Plot the heatmap of mzrt profiles |
plotint |
plot the information of intergretion |
plotintslope |
plot the slope information of intergretion |
plotkms |
plot the kendrick mass defect diagram |
plotmr |
plot the scatter plot for peaks list with threshold |
plotmrc |
plot the diff scatter plot for one xcmsset objects with threshold between two groups |
plotms |
plot GC/LC-MS data as a heatmap with TIC |
plotmsrt |
Plot EIC of certain m/z and return dataframe for intergration |
plotmz |
plot GC/LC-MS data as scatter plot |
plotpca |
plot the PCA for multiple samples |
plotpeak |
plot intensity of peaks across samples or samples across peaks |
plotridge |
plot ridgeline density plot |
plotridges |
Relative Log Abundance Ridge (RLAR) plots for samples or peaks |
plotrla |
Relative Log Abundance (RLA) plots |
plotrsd |
plot the rsd influnces of data in different groups |
plotrtms |
Plot mass spectrum of certain retention time and return mass spectrum vector (MSP file) for NIST search |
plotrug |
plot 1-d density for multiple samples |
plotsms |
Plot the intensity distribution of GC-MS |
plotsub |
Plot the backgrond of data |
plott |
plot GC-MS data as a heatmap for constant speed of temperature rising |
plottic |
Plot Total Ion Chromatogram (TIC) |
qbatch |
Get the MIR from the file |
runMDPlot |
Shiny application for interactive mass defect plots analysis |
runsccp |
Shiny application for Short-Chain Chlorinated Paraffins analysis |
sccp |
Short-Chain Chlorinated Paraffins(SCCPs) peaks infomation for quantitative analysis |
submd |
Get the differences of two GC/LC-MS data |
svabatch |
Plot the influnces of DoE and Batch effects on each peaks |
svacor |
Surrogate variable analysis(SVA) to correct the unknown batch effects |
svadata |
Filter the data with p value and q value |
svapca |
Principal component analysis(PCA) for SVA corrected data and raw data |
svaplot |
Filter the data with p value and q value and show them |
svaupload |
Get the corrected data after SVA for metabolanalyst |
TBBPA |
Demo data for TBBPA metabolism in Pumpkin |
writeMSP |
Write MSP files for NIST search |
xrankanno |
Perform MS/MS X rank annotation for mgf file |