Updated analysis: focal cn module- remove bit putting germline sex from WGS to WXS samples

[jharenza]

What analysis module should be updated and why?

Focal CN - remove bit putting germline sex from WGS to WXS samples, since we do this upstream in the histologies file preparation

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

Remove

OpenPedCan-analysis/analyses/focal-cn-file-preparation/01-add-ploidy-cnvkit.Rmd

Lines 31 to 57 in 029baa6

	# Filter to WXS tumor with no germline sex estimate
	no_estimate <- histologies_df %>%
	filter(sample_type == "Tumor" & experimental_strategy == "WXS" &
	is.na(germline_sex_estimate)) %>%
	select(-germline_sex_estimate)
	# Extract participant ID with no germline sex estimate
	no_estimate_participants <- no_estimate %>%
	pull(Kids_First_Participant_ID) %>%
	unique()
	# Find out matching WGS
	# Use Kids_First_Participant_ID for filtering samples that have WGS, when WXS was performed
	no_estimate_participants_match_wgs <- histologies_df %>%
	filter(Kids_First_Participant_ID %in% no_estimate_participants &
	experimental_strategy == "WGS" & sample_type == "Tumor") %>%
	select(Kids_First_Participant_ID, germline_sex_estimate)
	# Merge data that was fixed with WGS germline sex estimate
	no_estimate_fixed_through_wgs <- left_join(no_estimate, no_estimate_participants_match_wgs
	, by = "Kids_First_Participant_ID") %>%
	filter(!is.na(germline_sex_estimate))
	# Identify data that was not fixed due to NA
	no_estimate_still_na <- left_join(no_estimate, no_estimate_participants_match_wgs
	, by = "Kids_First_Participant_ID") %>%
	filter(is.na(germline_sex_estimate))

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

When do you expect the revised analysis will be completed?

Who will complete the updated analysis?

[jharenza]

#592 related

[jharenza]

rokitalab#22