differentialAbundanceTestMS: differentialAbundanceTestMS

In heuselm/igseqr: Integrate MiXCR BCR/IG-Seq and DIA-MS data to profile immune repertoire evolution

differentialAbundanceTestMS

Description

test differential abundance of proteins, clones and clone groups in DIA-MS data on precursor level

Usage

differentialAbundanceTestMS(
  DIA_resultset,
  study_design_external = NULL,
  comparison_matrix = matrix(c("AP_m11_tF", "AP_m11_t0", "AP_m12_tF", "AP_m12_t0",
    "AP_m1_tF", "AP_m1_t0", "AP_m2_tF", "AP_m2_t0"), ncol = 2, byrow = TRUE),
  write_preprocessing_results = TRUE,
  write_diffTable_csv_protein = TRUE,
  write_diffTable_csv_precursor = TRUE,
  imputation_percentile = 0.001,
  imputation_rnorm_sd = 0.2,
  overview_label_prefix = "IGSeq_M1imm_APMS_batch1_t3t0",
  plot_pdf = TRUE,
  plot_html = TRUE,
  prot_highlight_tag = "IGSeq"
)

Arguments

DIA_resultset	DIA-MS resultset imported by importDIAresults function.
study_design_external	Alternative study design overwriting the study design in DIA_resultset containing columns filename
comparison_matrix	A matrix defining the comparisons to be run. Column one contains the condition in the counter of each comparison, column two condition in the denominator of the comparison. Positive log2FCs will mean higher signal in counter condition listed in column 1. For possible values, check unique(DIA_resultset$study_design$condition). The data will be subset to the conditions specified in the comparison matrix.
write_preprocessing_results	Whether the intermediate results of each pairwise comparison shall be written. Separate subfolders will be generated. Default: FALSE
imputation_percentile	Percentile of non-0 quantitative values that the normal distribution for missing value imputation shall be centered on. Default: 0.001. Check imputation_histogram.pdf output for parameter selection.
imputation_rnorm_sd	Standard deviation (~width) of the normal distribution for missing value imputation. Check imputation_histogram.pdf output for parameter selection.
overview_label_prefix	Prefix label for the differential abundance overview .pdf and interactive .html plots
plot_pdf	Whether to plot summary of the differential tests.
plot_html	If plotting summary, whether to also generate interactive summary of the differential tests.
prot_highlight_tag	tag that determines which protein.groups get highlighted
write_csv_protein	Whether to write differential abundance testing result table summarized to protein level (csv). Default: TRUE
write_csv_precursor	Whether to write differential abundance testing result table containing precursor level information (csv). Default: FALSE

Value

DIA_resultset with appended element $differentialAbundanceTestResults with tables $diffTestRes_prec $diffTestRes_prot $comparison_matrix $data_source $study_design $data_long $data_matrix_log2 $data_matrix_log2_imp

heuselm/igseqr documentation built on March 19, 2022, 7:28 p.m.