R/.ipynb_checkpoints/rifi_stats-checkpoint.r

In CyanolabFreiburg/rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

# =========================================================================
# rifi_stats        Conveniently wraps all statistical prediction steps
# -------------------------------------------------------------------------
#'
#' rifi_stats wraps the functions: predict_ps_itss, apply_Ttest_delay, 
#' apply_ancova, apply_event_position, apply_t_test, fold_change,
#' apply_manova, apply_t_test_ti and gff3_preprocess.
#' 
#' @param inp SummarizedExperiment: the input data frame with correct format.
#' @param dista integer: the maximal distance allowed between two successive
#' fragments. Default is the auto generated value.
#' @param path path: to the directory containing the gff3 file.
#' 
#' @return the SummarizedExperiment object: checked, and with position, ID,
#'  strand, intensity, probe_TI, flag, position_segment, delay, half_life, 
#'  TI_termination_factor, delay_fragment, velocity_fragment, intercept, 
#'  slope, HL_fragment, HL_mean_fragment, intensity_fragment, intensity_mean_fragment,
#'  TU, TI_termination_fragment, TI_mean_termination_factor, seg_ID, pausing_site, 
#'  iTSS_I, ps_ts_fragment, event_ps_itss_p_value_Ttest, p_value_slope, delay_frg_slope,
#'  velocity_ratio, event_duration, event_position, FC_HL, FC_fragment_HL, p_value_HL, 
#'  FC_intensity, FC_fragment_intensity, p_value_intensity, FC_HL_intensity, 
#'  FC_HL_intensity_fragment, FC_HL_adapted, synthesis_ratio, synthesis_ratio_event, 
#'  p_value_Manova, p_value_TI, TI_fragments_p_value
#' }
#' 
#' @seealso `predict_ps_itss`
#' @seealso `apply_Ttest_delay`
#' @seealso `apply_ancova`
#' @seealso `apply_event_position`
#' @seealso `apply_t_test`
#' @seealso `fold_change`
#' @seealso `apply_manova`
#' @seealso `apply_t_test_ti`
#' @seealso `gff3_preprocess`
#' 
#' @examples
#' data(fragmentation_minimal)
#' rifi_stats(inp = fragmentation_minimal, dista = 300, 
#' path = gzfile(system.file("extdata", "gff_e_coli.gff3.gz",
#' package = "rifi")))
#' 
#' @export

rifi_stats <- function(inp, dista = 300, path) {
  message("running predict_ps_itss...")
  probe <- predict_ps_itss(inp = inp, maxDis = dista)
  message("running apply_Ttest_delay...")
  probe <- apply_Ttest_delay(inp = probe)
  message("running apply_ancova...")
  probe <- apply_ancova(inp = probe)
  message("running apply_event_position...")
  probe <- apply_event_position(inp = probe)
  message("running apply_t_test...")
  probe <- apply_t_test(inp = probe)
  message("running fold_change...")
  probe <- fold_change(inp = probe)
  message("running apply_manova...")
  probe <- apply_manova(inp = probe)
  message("running apply_t_test_ti...")
  probe <- apply_t_test_ti(inp = probe)
  metadata(probe)$annot <- gff3_preprocess(path)
  probe
}