Updated analysis: CNV deep deletions

[kgaonkar6]

What analysis module should be updated and why?

update focal-cn-file-preparation
and
rerun ocnoprint-landscape

What changes need to be made? Please provide enough detail for another participant to make the update.

Change:

OpenPBTA-analysis/analyses/focal-cn-file-preparation/04-prepare-cn-file.R

Lines 240 to 247 in 6bf301e

	# Merge and annotated no X&Y
	autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
	txdb_exons = tx_exons) %>%
	# mark possible amplifications in autosomes
	dplyr::mutate(status = dplyr::case_when(
	copy_number > (2 * ploidy) ~ "amplification",
	TRUE ~ status
	))

To:

# Merge and annotated no X&Y
autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
                                                   txdb_exons = tx_exons) %>%
  # mark possible amplifications and deep loss in autosomes
  dplyr::mutate(status = dplyr::case_when(
    copy_number > (2 * ploidy) ~ "amplification",
    copy_number == 0  ~ "deep loss",
    TRUE ~ status
  ))

Change:

OpenPBTA-analysis/analyses/focal-cn-file-preparation/04-prepare-cn-file.R

Lines 265 to 267 in 6bf301e

	# Merge and annotated no X&Y
	sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
	txdb_exons = tx_exons)

To:

  sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
                                                      txdb_exons = tx_exons) %>%
  # mark possible deep loss in sex chromosome
  dplyr::mutate(status = case_when(
    copy_number == 0  ~ "deep loss",
   TRUE ~ status
  ))

What input data should be used? Which data were used in the version being updated?

pbta-cnv-consensus.seg.gz v19

When do you expect the revised analysis will be completed?

~1 day

Who will complete the updated analysis?

@kgaonkar6

cc @jharenza @jaclyn-taroni for input

[jharenza]

closed with #1101