R/deprecated.R

Defines functions getfeaturesanova getfeaturest plote getmzrt2 getupload3 getupload2 getupload svaupload svaplot svapca svadata svacor svabatch gettimegrouprep gettechrep getsim getgrouprep getbiotechrep getbgremove

Documented in getbgremove getbiotechrep getfeaturesanova getfeaturest getgrouprep getmzrt2 getsim gettechrep gettimegrouprep getupload getupload2 getupload3 plote svabatch svacor svadata svapca svaplot svaupload

#' Get the peak list with blank samples' peaks removed
#' @param xset the xcmsset object with blank and certain group samples' data
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @param file file name for further annotation, default NULL
#' @param rsdcf rsd cutoff for peaks, default 30
#' @param inscf intensity cutoff for peaks, default 1000
#' @return diff report
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' xset <- getdata(cdfpath, pmethod = ' ')
#' getbgremove(xset)
#' }
#' @export
getbgremove <-
        function(xset,
                 method = "medret",
                 intensity = "into",
                 file = NULL,
                 rsdcf = 30,
                 inscf = 1000) {
                .Deprecated("getdoe")
                message("This function has been deprecated and you could use getdoe to remove background.")
        }

#' Get the report for biological replicates.
#' @param xset the xcmsset object which for all of your technique replicates for bio replicated sample in single group
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @param file file name for further annotation, default NULL
#' @param rsdcf rsd cutoff for peaks, default 30
#' @param inscf intensity cutoff for peaks, default 0
#' @return dataframe with mean, standard deviation and RSD for those technique replicates & biological replicates combined with raw data
#' @export
getbiotechrep <-
        function(xset,
                 method = "medret",
                 intensity = "into",
                 file = NULL,
                 rsdcf = 30,
                 inscf = 1000) {
                .Deprecated("getdoe")
                message("This function has been deprecated and you could use getdoe to process data.")
        }

#' Get the report for samples with biological and technique replicates in different groups
#' @param xset the xcmsset object all of samples with technique replicates
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @param file file name for the peaklist to MetaboAnalyst
#' @param rsdcf rsd cutoff for peaks, default 30
#' @param inscf intensity cutoff for peaks, default 1000
#' @return dataframe with mean, standard deviation and RSD for those technique replicates & biological replicates combined with raw data in different groups if file are defaults NULL.
#' @export
getgrouprep <-
        function(xset,
                 file = NULL,
                 method = "medret",
                 intensity = "into",
                 rsdcf = 30,
                 inscf = 1000) {
                .Deprecated("getdoe")
                message("This function has been deprecated and you could use getdoe to process data.")
        }

#' output the similarity of two dataset
#' @param xset1 the first dataset
#' @param xset2 the second dateset
#' @return similarity on retention time and rsd %
#' @export
getsim <- function(xset1, xset2) {
        .Deprecated()
        message("This function has been deprecated.")
}

#' Get the report for technique replicates.
#' @param xset the xcmsset object which for all of your technique replicates for one sample
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @param file file name for further annotation, default NULL
#' @param rsdcf rsd cutoff for peaks, default 30
#' @param inscf intensity cutoff for peaks, default 1000
#' @return dataframe with mean, standard deviation and RSD for those technique replicates combined with raw data
#' @export
gettechrep <-
        function(xset,
                 method = "medret",
                 intensity = "into",
                 file = NULL,
                 rsdcf = 30,
                 inscf = 1000) {
                .Deprecated("getdoe")
                message("This function has been deprecated and you could use getdoe to process data.")
        }

#' Get the time series or two factor DoE report for samples with biological and technique replicates in different groups
#' @param xset the xcmsset object all of samples with technique replicates in time series or two factor DoE
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @param file file name for the peaklist to MetaboAnalyst
#' @param rsdcf rsd cutoff for peaks, default 30
#' @param inscf intensity cutoff for peaks, default 1000
#' @return dataframe with time series or two factor DoE mean, standard deviation and RSD for those technique replicates & biological replicates combined with raw data in different groups if file are defaults NULL.
#' @export
gettimegrouprep <-
        function(xset,
                 file = NULL,
                 method = "medret",
                 intensity = "into",
                 rsdcf = 30,
                 inscf = 1000) {
                .Deprecated("getdoe")
                message("This function has been deprecated and you could use getdoe to process data.")
        }

#' Plot the influnces of DoE and Batch effects on each peaks
#' @param df data output from `svacor` function
#' @param dfsv data output from `svaplot` function for corrected data
#' @param dfanova data output from `svaplot` function for raw data
#' @return influnces plot
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' df <- svacor(xset3)
#' dfsv <- svaplot(xset3)
#' dfanova <- svaplot(xset3, pqvalues = "anova")
#' svabatch(df,dfsv,dfanova)
#' }
#' @seealso \code{\link{svacor}}, \code{\link{svaplot}}, \code{\link{svapca}}
#' @export
svabatch <- function(df, dfsv, dfanova) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}

#' Surrogate variable analysis(SVA) to correct the unknown batch effects
#' @param xset xcmsset object
#' @param lv group information
#' @param method parameter for groupval function
#' @param intensity parameter for groupval function
#' @details this is used for reviesed version of SVA to correct the unknown batch effects
#' @return list object with various components such raw data, corrected data, signal part, random errors part, batch part, p-values, q-values, mass, rt, Posterior Probabilities of Surrogate variables and Posterior Probabilities of Mod. If no surrogate variable found, corresponding part would miss.
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' df <- svacor(xset3)
#' }
#' @seealso \code{\link{svapca}}, \code{\link{svaplot}}, \code{\link{svabatch}}
#' @export
svacor <- function(xset,
                   lv = NULL,
                   method = "medret",
                   intensity = "into") {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}

#' Filter the data with p value and q value
#' @param list results from svacor function
#' @param pqvalues method for ANOVA or SVA
#' @param pt threshold for p value, default is 0.05
#' @param qt threshold for q value, default is 0.05
#' @return data, corrected data, mz and retention for fileted data
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' df <- svacor(xset3)
#' svadata(df)
#' }
#' @export
svadata <- function(list,
                    pqvalues = "sv",
                    pt = 0.05,
                    qt = 0.05) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}

#' Principal component analysis(PCA) for SVA corrected data and raw data
#' @param list results from svacor function
#' @param center parameters for PCA
#' @param scale parameters for scale
#' @param lv group information
#' @return plot
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' df <- svacor(xset3)
#' svapca(df)
#' }
#' @seealso \code{\link{svacor}}, \code{\link{svaplot}}, \code{\link{svabatch}}
#' @export
svapca <- function(list,
                   center = T,
                   scale = T,
                   lv = NULL) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}

#' Filter the data with p value and q value and show them
#' @param list results from svacor function
#' @param pqvalues method for ANOVA or SVA
#' @param pt threshold for p value, default is 0.05
#' @param qt threshold for q value, default is 0.05
#' @param lv group information
#' @param index index for selected peaks
#' @return heatmap for the data
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' df <- svacor(xset3)
#' svaplot(df)
#' }
#' @seealso \code{\link{svacor}}, \code{\link{svapca}}, \code{\link{svabatch}}
#' @export
svaplot <- function(list,
                    pqvalues = "sv",
                    pt = 0.05,
                    qt = 0.05,
                    lv = NULL,
                    index = NULL) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}

#' Get the corrected data after SVA for metabolanalyst
#' @param xset xcmsset object
#' @param lv group information
#' @return csv files for both raw and corrected data for metabolanalyst if SVA could be applied
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file("cdf", package = "faahKO")
#' cdffiles <- list.files(cdfpath, recursive = TRUE, full.names = TRUE)
#' xset <- xcmsSet(cdffiles)
#' xset <- group(xset)
#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden")
#' xset2 <- group(xset2, bw = 10)
#' xset3 <- fillPeaks(xset2)
#' svaupload(xset3)
#' }
#' @export
svaupload <- function(xset, lv = NULL) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use mzrtsim package for batch effect correction."
        )
}
#' Get the csv files from xcmsset/XCMSnExp/list object
#' @param xset the xcmsset/XCMSnExp/list object which you want to submitted to Metaboanalyst
#' @param method parameter for groupval function
#' @param value parameter for groupval function
#' @param name file name
#' @param type m means  Metaboanalyst, a means xMSannotator, o means full infomation csv
#' @param mzdigit m/z digits of row names of data frame
#' @param rtdigit retention time digits of row names of data frame
#' @return dataframe with data needed for Metaboanalyst/xMSannotator/pmd if your want to perform local analysis.
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file('cdf', package = 'faahKO')
#' xset <- getdata(cdfpath, pmethod = ' ')
#' getupload(xset)
#' }
#' @seealso \code{\link{getdata}}, \code{\link{getmzrt}}
#' @export
getupload <-
        function(xset,
                 method = "medret",
                 value = "into",
                 name = "Peaklist",
                 type = 'm',
                 mzdigit = 4,
                 rtdigit = 1) {
                .Deprecated()
                message("This function has been deprecated and you could use getmzrt to get csv file.")
        }
#' Get the csv files to be submitted to Metaboanalyst
#' @param xset a XCMSnExp object with processed data which you want to submitted to Metaboanalyst
#' @param value value for `xcms::featureValues`
#' @param name file name
#' @return dataframe with data needed for Metaboanalyst if your want to perform local analysis.
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file('cdf', package = 'faahKO')
#' xset <- getdata2(cdfpath)
#' getupload2(xset)
#' }
#' @seealso \code{\link{getdata2}},\code{\link{getupload}}, \code{\link{getmzrt2}}
#' @export
getupload2 <- function(xset, value = "into", name = "Peaklist") {
        .Deprecated()
        message("This function has been deprecated and you could use getupload to get csv file.")
}

#' Get the csv files to be submitted to Metaboanalyst
#' @param list list with data as peaks list, mz, rt and group information
#' @param name file name
#' @return dataframe with data needed for Metaboanalyst if your want to perform local analysis.
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file('cdf', package = 'faahKO')
#' xset <- getdata2(cdfpath,
#' ppp = xcms::MatchedFilterParam(),
#' rtp = xcms::ObiwarpParam(),
#' gpp = xcms::PeakDensityParam())
#' xset <- enviGCMS::getmzrt2(xset)
#' getupload3(xset)
#' }
#' @seealso \code{\link{getmzrt}}, \code{\link{getmzrt2}}
#' @export
getupload3 <- function(list, name = "Peaklist") {
        .Deprecated()
        message("This function has been deprecated and you could use getupload to get csv file.")
}
#' Get the mzrt profile and group information for batch correction and plot as a list for xcms 3 object
#' @param xset a XCMSnExp object with processed data
#' @param name file name for csv file, default NULL
#' @return list with rtmz profile and group infomation
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file('cdf', package = 'faahKO')
#' xset <- getdata2(cdfpath,
#' ppp = xcms::MatchedFilterParam(),
#' rtp = xcms::ObiwarpParam(),
#' gpp = xcms::PeakDensityParam())
#' getmzrt2(xset)
#' }
#' @seealso \code{\link{getdata2}},\code{\link{getupload2}}, \code{\link{getmzrt}}, \code{\link{getdoe}},\code{\link{getmzrtcsv}}
#' @export
getmzrt2 <- function(xset, name = NULL) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use getmzrt to get list object or csv file."
        )
}
#' plot EIC and boxplot for all peaks and return diffreport
#' @param xset xcmsset object
#' @param name filebase of the sub dir
#' @param test 't' means two-sample welch t-test, 't.equalvar' means two-sample welch t-test with equal variance, 'wilcoxon' means rank sum wilcoxon test, 'f' means F-test, 'pairt' means paired t test, 'blockf' means Two-way analysis of variance, default 't'
#' @param nonpara 'y' means using nonparametric ranked data, 'n' means original data
#' @param ... other parameters for `diffreport`
#' @return diffreport and pdf figure for EIC and boxplot
#' @examples
#' \dontrun{
#' library(faahKO)
#' cdfpath <- system.file('cdf', package = 'faahKO')
#' xset <- getdata(cdfpath, pmethod = ' ')
#' plote(xset)
#' }
#' @export
plote <- function(xset,
                  name = "test",
                  test = "t",
                  nonpara = "n",
                  ...) {
        .Deprecated()
        message(
                "This function will be deprecated and you could use getmzrt to get related object to plot EIC."
        )
        gt <- xcms::groups(xset)
        a <-
                xcms::diffreport(
                        xset,
                        filebase = name,
                        eicmax = nrow(gt),
                        nonpara = nonpara,
                        ...
                )
        return(a)
}

#' Get the features from t test, with p value, q value, rsd and power restriction
#' @param list list with data as peaks list, mz, rt and group information (two groups)
#' @param power defined power
#' @param pt p value threshold
#' @param qt q value threshold, BH adjust
#' @param n sample numbers in one group
#' @param imputation parameters for `getimputation` function method
#' @return dataframe with peaks fit the setting above
#' @export
getfeaturest <- function(list,
                         power = 0.8,
                         pt = 0.05,
                         qt = 0.05,
                         n = 3,
                         imputation = "l") {
        .Deprecated()
        message(
                "This function has been deprecated and you could use getpower to calculate post-hoc power for each peaks."
        )
}

#' Get the features from anova, with p value, q value, rsd and power restriction
#' @param list list with data as peaks list, mz, rt and group information (more than two groups)
#' @param power defined power
#' @param pt p value threshold
#' @param qt q value threshold, BH adjust
#' @param n sample numbers in one group
#' @param ng group numbers
#' @param inscf Log intensity cutoff for peaks across samples. If any peaks show a intensity higher than the cutoff in any samples, this peaks would not be filtered. default 5
#' @param rsdcf the rsd cutoff of all peaks in all group
#' @param imputation parameters for `getimputation` function method
#' @param index the index of peaks considered, default NULL
#' @return dataframe with peaks fit the setting above
#' @export
getfeaturesanova <- function(list,
                             power = 0.8,
                             pt = 0.05,
                             qt = 0.05,
                             n = 3,
                             ng = 3,
                             rsdcf = 100,
                             inscf = 5,
                             imputation = "l",
                             index = NULL) {
        .Deprecated()
        message(
                "This function has been deprecated and you could use getpower to calculate post-hoc power for each peaks."
        )
}

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enviGCMS documentation built on July 8, 2020, 5:52 p.m.