stats.md

Proposed panel vs desired targets

Logical checks

stopifnot(!panel$uncovered | !panel$covered)
stopifnot(!panel$covered | panel$has.coverage)

All affected regions of length at least 2 are for estimating blood cell counts

stopifnot(all(!(panel$uncovered & panel$end-panel$start > 1) | panel$source == "blood-cell-types"))

For each blood cell type, at most 20% of regions are affected

kable(with(panel[panel$source == "blood-cell-types",], stats.table(uncovered, details)))

	affected	total	pct
Blood-Granul	2	25	8
Blood-T	2	25	8
Blood-B	4	25	16
Blood-Mono+Macro	5	25	20

For each blood cell type, at most 8% of the regions have no coverage at all

kable(with(panel[panel$source == "blood-cell-types",], stats.table(!has.coverage, details)))

	affected	total	pct
Blood-Granul	2	25	8
Blood-Mono+Macro	2	25	8

For most remaining sources, less than 2% of CpG sites affected

kable(with(panel[panel$source != "blood-cell-types",],
           stats.table(uncovered,source)))

	affected	total	pct
alcohol-consumption	1	314	0.3
ancestry	6	1550	0.4
episcores	5	971	0.5
dunedin-pace	2	173	1.2
dunedin-poam38	2	46	4.3

kable(with(panel[panel$source != "blood-cell-types",],
           stats.table(!has.coverage,source)))

	affected	total	pct
alcohol-consumption	1	314	0.3
ancestry	6	1550	0.4
episcores	5	971	0.5
dunedin-pace	2	173	1.2
dunedin-poam38	2	46	4.3