M&M ASH benchmark Part III¶

This is a continuation of Part II where instead of looking at 1 causal SNP of PVE = 0.05 I look at 2 causal SNPs with total PVE set to 0.15.

Conclusion¶

The expected increase trend in power of singleton, identity and shared is completely reversed!

./finemap.dsc --target sanity_check -o sanity_check3 -c 39

%cd ~/GIT/github/mnm-twas/dsc

/home/gaow/GIT/github/mnm-twas/dsc

library('dscrutils')
out = dscquery('sanity_check3', "hundred_data.dataset sharing_pattern.n_signal susie_scores.total susie_scores.valid susie_scores.size susie_scores.purity susie_scores.top", groups="sharing_pattern: singleton, identity, shared")

Loading dsc-query output from CSV file.
Reading DSC outputs:
 - sharing_pattern.n_signal: extracted atomic values
 - susie_scores.total: extracted atomic values
 - susie_scores.valid: extracted atomic values
 - susie_scores.size: extracted atomic values
 - susie_scores.purity: extracted atomic values
 - susie_scores.top: extracted atomic values

head(out)

out[,c(4,5,6,7,8,9)] = as.numeric(as.matrix(out[,c(4,5,6,7,8,9)]))
res = out[,c(3,4,5,6,7,8,9)]
colnames(res) = c('pattern', 'total_true', 'total', 'valid', 'size', 'purity', 'top_hit')

Purity of CS¶

aggregate(purity~pattern, res, mean)

Size of CS¶

aggregate(size~pattern, res, median)

Power¶

valid = aggregate(valid ~ pattern, res, sum)
total_true = aggregate(total_true ~ pattern, res, sum)
power = merge(valid, total_true, by = "pattern")
power$power = power$valid/power$total_true
power

FDR¶

valid = aggregate(valid ~ pattern, res, sum)
total = aggregate(total ~ pattern, res, sum)
fdr = merge(valid, total, by = "pattern")
fdr$fdr = (fdr$total - fdr$valid)/fdr$total
fdr

Top-hit rate (how often the strongest SNP is causal)¶

top_hit = aggregate(top_hit ~ pattern, res, sum)
total_true = aggregate(total_true ~ pattern, res, sum)
top_rate = merge(top_hit, total_true, by = "pattern")
top_rate$top_rate = top_rate$top_hit/top_rate$total_true
top_rate

pattern	valid	total_true	power
identity	148	200	0.740
shared	126	200	0.630
singleton	157	200	0.785

pattern	valid	total	fdr
identity	148	157	0.05732484
shared	126	135	0.06666667
singleton	157	159	0.01257862

pattern	top_hit	total_true	top_rate
identity	79	200	0.395
shared	75	200	0.375
singleton	77	200	0.385

DSC	hundred_data.dataset	sharing_pattern	sharing_pattern.n_signal	susie_scores.total	susie_scores.valid	susie_scores.size	susie_scores.purity	susie_scores.top
1	~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds	singleton	2	2	2	7.5	0.997902685565869	1
1	~/Documents/GTExV8/Toys/Thyroid.ENSG00000031823.RDS	singleton	2	1	1	1	1	1
1	~/Documents/GTExV8/Toys/Thyroid.ENSG00000062194.RDS	singleton	2	2	2	8.5	0.980400377080065	1
1	~/Documents/GTExV8/Toys/Thyroid.ENSG00000073150.RDS	singleton	2	1	1	7	0.984587614689054	0
1	~/Documents/GTExV8/Toys/Thyroid.ENSG00000078319.RDS	singleton	2	1	1	2	0.999964909747404	0
1	~/Documents/GTExV8/Toys/Thyroid.ENSG00000081277.RDS	singleton	2	1	1	25	0.966136167252649	0

pattern	purity
identity	0.9652615
shared	0.9714742
singleton	0.9612232

pattern	size
identity	7.25
shared	4.75
singleton	7.00