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#' Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
#'
#' @description Provides functionality for quality control processing and
#' statistical analysis of mass spectrometry (MS) omics data, in particular
#' proteomic (either at the peptide or the protein level), lipidomic, and
#' metabolomic data, as well as RNA-seq based count data and nuclear magnetic
#' resonance (NMR) data. This includes data transformation, specification of
#' groups that are to be compared against each other, filtering of features
#' and/or samples, data normalization, data summarization (correlation, PCA),
#' and statistical comparisons between defined groups.
#'
#' @docType package
#'
#' @import methods
#' @importFrom Rcpp evalCpp
#' @importFrom stats anova aov as.formula binomial complete.cases cor dist ecdf formula glm hclust lm mad median model.matrix na.omit p.adjust.methods pbinom pchisq qchisq quantile runif sd setNames t.test var
#' @importFrom utils capture.output combn data head stack tail
#' @importFrom dplyr .data
#' @useDynLib pmartR
#' @name pmartR
#'
#' @return No return value, used to appease R CMD check.
NULL
utils::globalVariables(
c(
".", ":=", ":::", "::",
"Absent", "Absent Count", "Absent Proportion", "Abundance",
"AveLogCPM", "baseMean", "Batch", "bins", "Biomolecule", "both_cov",
"both_me", "color", "Color", "Comparison", "Count", "Count_biomolecules",
"Count_First_Group", "Count_Second_Group", "counts", "CV", "Data Type",
"dcast", "desc", "Direction", "dispersion", "dispFit", "dispGeneEst",
"el", "Flags", "fold_change", "Fold_change", "Fold_change_flag",
"Freq", "frequency_counts", "Group", "Group.x", "Group.y", "i",
"insufficient", "lcpm", "LibrarySize", "Log2.md", "melt",
"metabolite_cname", "Metric", "Min_obs", "molecule", "mols_used_in_norm",
"n", "N", "n_combine", "n_control", "n_cov", "n_groups", "n_me",
"n_peps_used", "n_test", "name", "Nested_DF", "NonZero",
"normalization_method", "nuff", "num_NA", "num_observations", "P_value",
"p_value_anova", "paired_diff", "Panel By Choice", "parameters", "PC1",
"PC2", "peps_per_pro", "Peptide", "posneg", "Present", "Present Count",
"Present Proportion", "ProportionNonZero", "Protein_Isoform",
"pval", "res", "Sample", "SampleID", "setnames", "sig", "Significance",
"skew", "SPANS_score", "ss_par", "Statistic", "subset_method", "survfit",
"Total", "Total_Counts", "Type", "v", "value", "values", "var1",
"var2", "variable", "whichtest", "x_disp", "x_fit", "y", "y_disp",
"y_fit", "biomolecule count", "cv abundance", "mean abundance",
"mean fold change", "median abundance", "observed count",
"observed proportion", "p_value_gtest", "proportion significant",
"proportion significant down", "proportion significant up",
"sample count", "sd fold change", "total count"
)
)
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