annotateMSdetection: annotateMSdetection

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

annotateMSdetection

Description

annotate MS detection of IGSeq clones based on DIA_resultset

Usage

annotateMSdetection(
  IGSeq_resultset = seq_r06_fasta,
  DIA_resultset = ms_r06,
  write_table = TRUE,
  n_prot_uniqueness_threshold = 1
)

Arguments

IGSeq_resultset	IgSeq resultset to be annotated with MS detection
DIA_resultset	DIA MS resultset based on which to annotate MS detection of the clones in IGSeq_resultset.
write_table	Whether to write .csv table of MS detection. Default: TRUE
n_prot_uniqueness_threshold	Uniqueness threshold to define clones detected with sufficient specificity. This may be useful to quantify clonal families with high homology with a certain degree of sharedness of the detectable peptide set. Defaults to 1, i.e. only peptides mapping to only one of the clones in the context of the current .fasta will be maintained for unique analysis

Value

IGSeq_resultset with added element step7_clonesMSdetection with tables $clones_detected and quantitative matrices across the MS runs in the DIA_resultset calculated from all mapped or only unique peptides according to the n_prot_uniqueness threshold set as parameter: $MS_abundance_allprecursors_mean, $MS_abundance_uniqueprecursors_mean. In addition, the study design of the DIA_resultset is used to aggregate and report quantities and frequency of observation (mean and sd of precursor intensities and n_rep) across conditions. There are calculated including only *unique* precursors (note n_prot_uniqueness_threshold parameter to modify this inclusion criterion). The result matrices are stored as list elements in the result object with names: MS_abundance_uniqueprecursors_mean_cond_rep, MS_abundance_uniqueprecursors_mean_cond, MS_abundance_uniqueprecursors_sd_cond, MS_detection_uniqueprecursors_nrep_cond, MS_abundance_uniqueprecursors_mean_long. Further, the study_design from the DIA_resultset is propagated to the resultset in slot $study_design

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