importIgSeq: summarizeIgSeqResults

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

summarizeIgSeqResults

Description

summarize MiXCR IgSeq results as structured by https://github.com/heuselm/igseq_workflow.git

Usage

importIgSeq(
  result_folder = ".",
  write_tables = TRUE,
  report_folder = "importIgSeq_log",
  summarize_in_pdfs = TRUE,
  chain_type_index_end = 4
)

Arguments

result_folder	Location of the IgSeq-workflow result folder.
write_tables	Switch whether the collected summary information should be output as .csv tables
summarize_in_pdfs	Whether the results are directly summarized via summarizeIgSeq function. Default: TRUE
chain_type_index_end	End character position in AllCHitsWithScore column to assign chain type. Default: 4 (differentiates isotypes, e.g. IGHG from IGHM). If set to 3, all isotypes will be considered IGH chains, w/o differentiation.

Value

IGSeq result object (list) with tables * step1_checkout_log * step2_histogram_log * step2_histogram_osq * step3_assemble_log * step4_align_log * step5_cloneAssembly_log" * step5_finalclones

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