pmfxcms | R Documentation |
A wrapper function for XCMS using common PMF platforms.
pmfxcms(
ExpDes = NULL,
MStag = "01.cdf",
idMSMStag = "02.cdf",
filetype = "cdf",
factorfile = "seq.csv",
cores = 4,
minpw = 3,
maxpw = 30,
filtPeaks = TRUE,
ppmerr = 35,
minTIC = 10,
outTIC = TRUE,
outPCA = TRUE,
pcut = 0.05,
p.adj = "BH",
snthresh = 10,
mzdiffquad = 0.5,
bwpre = 3,
bwpost = 1,
minfrac = 0.15,
fwhm = 3,
maxt = NULL,
step = NULL,
rtcor = "loess",
seqskip = 0,
regroup = FALSE,
rem.files = NULL
)
ExpDes |
R object generated by RAMClustR::defineExperiment function. |
MStag |
Character: "01.cdf" the text string used to recognize xmcs files as MS (low collision energy) when using indiscriminant MS/MS (MSE, AIF, ...) |
idMSMStag |
Character: "02.cdf",the text string used to recognize xmcs files as MS/MS (high collision energy) when using indiscriminant MS/MS (MSE, AIF, ...) |
filetype |
Character "cdf", The file extension - will be appended to file names in the csv 'factor file'. case insensitive. |
factorfile |
Character "seq.csv", The csv file containing filename (column 1) and sample name (column 2), Sample names can contain a delimitor separating factors, but all samples must contain the same number of factors (delimitors) |
cores |
Integer default = 4, how many computer cores to use in processing |
minpw |
Numerica (3) minimum peak width in seconds |
maxpw |
Numeric (30) maximum peak width in seconds |
filtPeaks |
Logical - TRUE. Should a filtering step be performed after peak detection to remove peaks out of minpw-maxpw range? |
ppmerr |
Numeric (35). If CentWave is used, what ppm error setting is used for feature detection? |
minTIC |
Numeric (10). If outTIC = TRUE, total ion signal minTIC fold lower than the median total ion signal are removed. |
outTIC |
Logical (TRUE). Should we remove injections based on total ion signal following peak detection? Uses outlier detection based on the distribution of signal values across samples and a cutoff defined by minTIC (on the low end of the distribution only) |
outPCA |
Logical (TRUE). Should we remove injections based on binned mass distribution after peak detection? Uses outlier detection on PC1 scores. |
pcut |
Numeric (0.05). p.value cutoff used to detect outliers. p values optionall corrected by p.adj (benhamini hochberg by default) |
p.adj |
character ("BH"). what pvalue false discovery rate correction to use on outlier detection steps. see ?p.adjust for options. |
snthresh |
numeric (10). signal to noise threshold used for feature detection (centWave or matchedFilter) |
mzdiffquad |
(0.5) mz bin size used for matchedFilter algorithm. |
bwpre |
numeric (3). bw parameter used in the feature grouping (correspondence) step BEFORE retention time adjustement |
bwpost |
numeric (1.5). bw parameter used in the feature grouping (correspondence) step AFTER retention time adjustment. If rt adjustment works well, we should be able to use a lower value than bwpre. |
minfrac |
numeric (0.15). minimum fraction of samples a feature must be found in (of full dataset) to be passed to final sample set. |
fwhm |
numeric (3). peak width at half height, used in matchedFilter algorithm. |
maxt |
numeric (NULL). retention time in seconds - peaks with retention times greater than maxt are excluded. |
step |
?? (NULL). |
rtcor |
character("loess"). one of NULL, "loess", "linear", "obiwarp", "nearest" NULL |
seqskip |
integer (0). Number of lines from top of factorfile to skip before starting. rarely used. |
regroup |
logical (FALSE). If true, try to load saved xcms object from 'datasets/' directory in working directory, skipping peak detection. |
rem.files |
vector of integer values. if regroup == TRUE, optional vector of sample numbers to remove. |
This function uses a template file as input to guide XCMS parameter selection.
Peak detection using centwave (LC-TOF) or matchedFilter (GC-Quad), density based peak grouping, loess rt correction, regrouping, and fillPeaks.
Additionally performs unsupervised removal of ultrawide chromatgoraphic peaks and outlier detection and removal after peak detection step.
an XCMS object is returned.
returns an xcms object
Corey Broeckling
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