prolfqua: Proteomics Label Free Quantification

#' @importFrom conflicted conflict_prefer
#' @importFrom forcats fct_relevel
#' @importFrom dplyr across all_of anti_join arrange bind_cols bind_rows case_when count desc distinct filter group_by group_by_at
#' @importFrom dplyr inner_join left_join mutate nest_by
#' @importFrom dplyr one_of rename select select_at starts_with summarize_at summarize ungroup vars
#'
#' @importFrom gridExtra grid.arrange
#' @importFrom ggplot2 aes aes_string element_text facet_grid ggplot ggtitle geom_boxplot
#' @importFrom ggplot2 geom_line geom_violin guides
#' @importFrom ggplot2 stat_summary scale_x_continuous scale_y_continuous theme
#'
#' @importFrom ggrepel geom_text_repel
#' @importFrom graphics par rect hist
#' @importFrom graphics abline pairs plot text
#' @importFrom grDevices colorRampPalette dev.off pdf png rainbow
#' @importFrom htmlwidgets saveWidget
#' @importFrom pheatmap pheatmap
#' @importFrom plotly ggplotly
#' @importFrom purrr map map2 map2_dbl map_lgl map_chr map_dbl reduce map_if map_dfc map_int map_df
#' @importFrom rlang := UQ sym syms .data
#' @importFrom stats as.formula cor
#' @importFrom stats .lm.fit glm model.matrix residuals
#' @importFrom tidyr gather nest nesting separate_rows spread unite unnest unnest_legacy separate
#' @importFrom tidyr pivot_wider
#' @importFrom tibble add_column as_tibble column_to_rownames tibble
#' @importFrom stats anova coef coefficients confint cor.test df.residual ecdf formula lm mad median medpolish
#' @importFrom stats na.omit p.adjust pbeta power.t.test prcomp predict pt qt quantile sd setNames sigma terms update vcov
#' @importFrom stringr str_trim
#' @importFrom utils combn data head read.csv tail unzip
#' @importFrom yaml write_yaml
NULL


## @importFrom vsn justvsn

#' Internal Functions by category
#' @family aggregation
#' @family benchmarking
#' @family concrete_configuration
#' @family configuration
#' @family deprecated
#' @family MaxQuant
#' @family modelling
#' @family FragPipe
#' @family plotting
#' @family preprocessing
#' @family stats
#' @family summary
#' @family transitionCorrelation
#' @family utilities
#' @family vignetteHelpers
#' @family workflows
#' @name INTERNAL_FUNCTIONS_BY_FAMILY
#'
NULL

#' Package Data
#' @family data
#' @name PACKAGE_DATA
NULL

# data_basicModel_p1807 <- prolfqua::basicModel_p1807
# usethis::use_data(data_basicModel_p1807, compress = TRUE, overwrite = TRUE)
# file.remove("data/basicModel_p1807.rda")

#' SAINT express output
#'
#' SAINT express output produced by running the function
#' \code{\link{runSaint}}
#'
#' @seealso \code{\link{runSaint}}
#' @family data
#' @keywords internal
#' @docType data
#' @format a linear model
"data_SAINTe_output"



#' Model for debugging
#' @family data
#' @keywords internal
#' @docType data
#' @format a linear model
"data_basicModel_p1807"

# #@usage data_basicModel_p1807 <- prolfqua_data("data_basicModel_p1807")

# data_benchmarkExample <- prolfqua::benchmarkDataExample
# usethis::use_data(data_benchmarkExample, compress = TRUE, overwrite = TRUE)
# file.remove("data/benchmarkDataExample.rda")

#' Benchmark data Example
#' @format A data frame
#' @family data
#' @docType data
#' @keywords internal
"data_benchmarkExample"

# #@usage data_benchmarkExample <- prolfqua_data("data_benchmarkExample")

# data_checksummarizationrobust87 <- prolfqua::checksummarizationrobust87
# usethis::use_data(data_checksummarizationrobust87, compress = TRUE, overwrite = TRUE)
# file.remove("data/checksummarizationrobust87.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_checksummarizationrobust87'

# #@usage data_checksummarizationrobust87 <- prolfqua_data("data_checksummarizationrobust87")

# data_checksummarizerobust <- prolfqua::checksummarizerobust
# usethis::use_data(data_checksummarizerobust, compress = TRUE, overwrite = TRUE)
# file.remove("data/checksummarizerobust.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_checksummarizerobust'

# #@usage data_checksummarizerobust <- prolfqua_data("data_checksummarizerobust")


# data_checksummarizerobust69 <- prolfqua::checksummarizerobust69
# usethis::use_data(data_checksummarizerobust69, compress = TRUE, overwrite = TRUE)
# file.remove("data/checksummarizerobust69.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
#'
'data_checksummarizerobust69'

# #@usage data_checksummarizerobust69 <- prolfqua_data("data_checksummarizerobust69")


#data_correlatedPeptideList <- prolfqua::correlatedPeptideList
#usethis::use_data(data_correlatedPeptideList, compress = TRUE, overwrite = TRUE)
#file.remove("data/correlatedPeptideList.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
#'
'data_correlatedPeptideList'

# #@usage data_correlatedPeptideList <- prolfqua_data("data_correlatedPeptideList")


# data_IonstarProtein_subsetNorm <- prolfqua::dataIonstarProtein_subsetNorm
# usethis::use_data(data_IonstarProtein_subsetNorm, compress = TRUE, overwrite = TRUE)
# file.remove("data/dataIonstarProtein_subsetNorm.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
#'
'data_IonstarProtein_subsetNorm'

# #@usage data_IonstarProtein_subsetNorm <- prolfqua_data("data_IonstarProtein_subsetNorm")




#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_interactionModel_p1807'

# #@usage data_interactionModel_p1807 <- prolfqua_data("data_interactionModel_p1807")


#data_ionstar <- ionstar
#usethis::use_data(data_ionstar, compress = TRUE, overwrite = TRUE)
#file.remove("data/ionstar.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_ionstar'

# #@usage data_ionstar <- prolfqua_data("data_ionstar")





# data_multigroupFC <- multigroupFCDATA
# usethis::use_data(data_multigroupFC,compress = TRUE, overwrite = TRUE)
# file.remove("data/multigroupFCDATA.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_multigroupFC'

# #@usage data_multigroupFC <- prolfqua_data("data_multigroupFC")

#' example data for check of scores produced based on confusion matrix
#' @family data
#' @docType data
#' @keywords internal
'data_test_confusion_matrix_scores'

# data_skylinePRMSample_A <- skylinePRMSampleData_A
# usethis::use_data(data_skylinePRMSample_A,compress = TRUE, overwrite = TRUE)
# file.remove("data/skylinePRMSampleData_A.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_skylinePRMSample_A'

# #@usage data_skylinePRMSample_A <- prolfqua_data("data_skylinePRMSample_A")


# data_skylineSRM_HL_A <- skylineSRM_HL_A
# usethis::use_data(data_skylineSRM_HL_A,compress = TRUE, overwrite = TRUE)
# file.remove("data/skylineSRM_HL_A.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_skylineSRM_HL_A'

# data_skylineSRM_HL_A <- prolfqua_data("data_skylineSRM_HL_A")
# data_skylineSRM_HL_A_new <- list()
# data_skylineSRM_HL_A_new$data <- data_skylineSRM_HL_A$data
# data_skylineSRM_HL_A_new$config_f <- function(){
#   skylineconfig_HL <- create_config_Skyline(isotopeLabel = "Isotope.Label",
#                                             ident_qValue = "annotation_QValue")
#   skylineconfig_HL$table$factors[["treatment_c"]] <- "Condition2"
#   skylineconfig_HL$table$factors[["time_c"]] <- "time"
#   skylineconfig_HL$table$is_response_transformed = FALSE
#   return(skylineconfig_HL)
# }
# data_skylineSRM_HL_A_new$analysis <- function(data,config ){
#   data$Area[data$Area == 0] <- NA
#   analysis <- setup_analysis(data, config)
#   return(analysis)
# }
# data_skylineSRM_HL_A <- data_skylineSRM_HL_A_new
# usethis::use_data(data_skylineSRM_HL_A,compress = TRUE, overwrite = TRUE)


#data_spectronautDIA250_A <- spectronautDIAData250_A
#usethis::use_data(data_spectronautDIA250_A,compress = TRUE, overwrite = TRUE)
#file.remove("data/spectronautDIAData250_A.rda")

#' example data for check
#' @family data
#' @docType data
#' @keywords internal
'data_spectronautDIA250_A'

# #@usage data_spectronautDIA250_A <- prolfqua_data("data_spectronautDIA250_A")

#' example of 2 Factor data
#' @family data
#' @docType data
#' @keywords internal
'data_Yeast2Factor'

# #@usage data_spectronautDIA250_A <- prolfqua_data("data_spectronautDIA250_A")