3. Output files - FinucaneLab/fine-mapping-inf GitHub Wiki
Possible outputs from running fine-mapping-inf are:
${PREFIX}.V.npz
${PREFIX}.Dsq.npz
${PREFIX}.susieinf.npz
${PREFIX}.susieinf.bgz
${PREFIX}.finemapinf.npz
${PREFIX}.finemapinf.bgz
${PREFIX}.finemapinf.config.bgz
.npz
files
Eigen decompositions
.npz
is the default file format for saving eigen decompositions of XtX. If --eigen-decomp-prefix
is specified, then .V.npz
and .Dsq.npz
will be saved to files. The arrays can be loaded with
V = numpy.load('${PREFIX}.V.npz')['arr_0']
Dsq = numpy.load('${PREFIX}.Dsq.npz')['arr_0']
Fine-mapping results
User can specify --save-npz
to save the fine-mapping results in the form of dictionaries to ${PREFIX}.susieinf.npz
and ${PREFIX}.finemapinf.npz
.
${PREFIX}.susieinf.npz
contains keys:
PIP, mu, omega, ssq, sigmasq, tausq, alpha, cred, lbf, lbf_variable
See susieinf/susieinf.py
for definitions of these keys.
${PREFIX}.finemapinf.npz
contains keys:
PIP, beta, se, sigmasq, tausq, alpha, models
See finemapinf/finemapinf/__init__.py
for definitions of these keys.
.bgz
files
The .bgz
files are bgzipped tab delimited text files.
.susieinf.bgz
file contains columns:
rsid, chromosome, position, allele1, allele2, maf
: basic variant infobeta, se, p
: marginal summary statisticsprob
: posterior inclusion probability for each variantalpha{1..L}, mu{1..L}, omega{1..L}, lbf_variable{1..L}
: component-wise parameters. Same definition as insusieinf/susieinf.py
alpha, tausq, sigmasq
: seesusieinf/susieinf.py
for definitionspost_mean
: computed assum(alpha{1..L}*mu{1..L},axis=1)+alpha
, posterior mean effect size (including infinitesimal effects)cs
: credible set ID, -1 means variant is not in any credible set
.finemapinf.bgz
file contains columns:
rsid, chromosome, position, allele1, allele2, maf
: basic variant infobeta, se, p
: marginal summary statisticsprob
: posterior inclusion probability for each variantpost_mean_cond, post_sd_cond
: posterior conditional mean and standard deviationalpha, tausq, sigmasq
: seefinemapinf/finemapinf/__init__.py
for definitionspost_mean
: posterior mean, computed aspost_mean_cond*prob
.finemapinf.config.bgz
file contains columns:
config
: causal configuration; 0-indexed; empty list represent the null modelprob
: posterior probability of configuration being causalprob
: posterior probability