deChar_multiGroup

This function is for multi-group lipid characteristics analysis. It identifies the differentially expressed lipid characteristics based on the user-selected characteristic.

Usage

deChar_multiGroup(
  processed_se,
  char,
  ref_group,
  post_hoc = c("One-way ANOVA", "Kruskal–Wallis test"),
  post_hoc_sig = c("pval", "padj"),
  post_hoc_p_cutoff = 0.05,
  transform = c("none", "log10", "square", "cube", "log2")
)

Arguments

processed_se

A SummarizedExperiment object constructed by as_summarized_experiment and processed by data_process.

char

Character. A lipid characteristic selected from the deChar list returned by list_lipid_char.

ref_group

Character. Group name of the reference group. It must be one of the group names in the group information table's group column.

post_hoc

Character. The method to statistic calculation. Allowed method include "One-way ANOVA" and "Kruskal–Wallis test". Default is 'One-way ANOVA'.

post_hoc_sig

Character. The p-value to be used for the statistically significant. Must be one of "pval" or "padj". Default is 'pval'.

post_hoc_p_cutoff

Numeric. Significant level. Default is 0.05.

transform

Character. Method for data transformation. Allowed methods include "none", "log10", "square", "cube", "log2". Select 'none' to skip data transformation. Default is 'log10'.

Value

Return a SummarizedExperiment object containing analysis results.

Examples

data("se_multiGroup")
processed_se <- data_process(
    se=se_multiGroup, exclude_missing=TRUE, exclude_missing_pct=70,
    replace_na_method='min', replace_na_method_ref=0.5,
    normalization='Percentage', transform='log10')
char_list <- list_lipid_char(processed_se)$deChar_list
#> There are 4 ratio characteristics that can be converted in your dataset.
print(char_list)
#>                               Lipid classification 
#>                                         "Category" 
#>                               Lipid classification 
#>                                       "Main.Class" 
#>                               Lipid classification 
#>                                        "Sub.Class" 
#>                               Lipid classification 
#>                                            "class" 
#>                              Fatty acid properties 
#>                                               "FA" 
#>                              Fatty acid properties 
#>                                             "FA.C" 
#>                              Fatty acid properties 
#>                        "FA.Chain.Length.Category1" 
#>                              Fatty acid properties 
#>                        "FA.Chain.Length.Category2" 
#>                              Fatty acid properties 
#>                        "FA.Chain.Length.Category3" 
#>                              Fatty acid properties 
#>                                            "FA.DB" 
#>                              Fatty acid properties 
#>                                            "FA.OH" 
#>                              Fatty acid properties 
#>                        "FA.Unsaturation.Category1" 
#>                              Fatty acid properties 
#>                        "FA.Unsaturation.Category2" 
#>                              Fatty acid properties 
#>                                          "Total.C" 
#>                              Fatty acid properties 
#>                                         "Total.DB" 
#>                              Fatty acid properties 
#>                                         "Total.FA" 
#>                              Fatty acid properties 
#>                                         "Total.OH" 
#>                    Physical or chemical properties 
#>                                "Bilayer.Thickness" 
#>                    Physical or chemical properties 
#>                                        "Bond.type" 
#>                    Physical or chemical properties 
#>                                 "Headgroup.Charge" 
#>                    Physical or chemical properties 
#>                              "Intrinsic.Curvature" 
#>                    Physical or chemical properties 
#>                                "Lateral.Diffusion" 
#>                    Physical or chemical properties 
#>                           "Transition.Temperature" 
#>                                 Cellular component 
#>                               "Cellular.Component" 
#>                                           Function 
#>                                         "Function" 
#>                                    Specific ratios 
#>                  "Chains Ether/Ester linked ratio" 
#>                                    Specific ratios 
#>                            "Chains odd/even ratio" 
#>                                    Specific ratios 
#>      "Ratio of Lysophospholipids to Phospholipids" 
#>                                    Specific ratios 
#> "Ratio of specific lipid class A to lipid class B" 
deChar_se <- deChar_multiGroup(
    processed_se, char='class', ref_group='ctrl', post_hoc='One-way ANOVA',
    post_hoc_sig='pval', post_hoc_p_cutoff=0.05, transform='log10')
#> There are 4 ratio characteristics that can be converted in your dataset.