CCmed_gwas: Estimate cross-condition mediation probability for a GWAS...
In kjgleason/CCmed: Cross-condition mediation analysis
Description
Usage
Arguments
Value
Description
For each SNP-cis-trans gene trio, estimate the probability of mediation.
Used to identify trans-associations of GWAS SNPs.
.
Usage
1
CCmed_gwas(cis_res, condcorr_res, cisID, condcorrID, ncond)
Arguments
cis_res
list object returned by running Primo on GWAS SNP cis-association statistics.
condcorr_res
list object returned by running Primo on conditional correlation statistics.
cisID
data.frame with two columns ("variant_id", "cis") that match the identifiers of
cis_res (i.e. rows in list element post_prob).
condcorrID
data.frame with two columns ("cis", "trans") that match the identifiers
of condcorr_res (i.e. rows in list element post_prob).
ncond
integer of the number of conditions required for mediation.
Value
data.frame with the following columns:
variant_id GWAS SNP identifier
cis cis-gene identifier
trans trans-gene identifier
ncond number of conditions required for mediation
prob_med probability of mediation in at least ncond conditions
The main element of interest for inference is the column prob_med.
kjgleason/CCmed documentation built on Nov. 14, 2019, 12:14 a.m.
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Description Usage Arguments Value
Description
For each SNP-cis-trans gene trio, estimate the probability of mediation. Used to identify trans-associations of GWAS SNPs. .
Usage
1 | CCmed_gwas(cis_res, condcorr_res, cisID, condcorrID, ncond)
|
Arguments
cis_res |
list object returned by running Primo on GWAS SNP cis-association statistics. |
condcorr_res |
list object returned by running Primo on conditional correlation statistics. |
cisID |
data.frame with two columns ("variant_id", "cis") that match the identifiers of
|
condcorrID |
data.frame with two columns ("cis", "trans") that match the identifiers
of |
ncond |
integer of the number of conditions required for mediation. |
Value
data.frame with the following columns:
variant_id | GWAS SNP identifier |
cis | cis-gene identifier |
trans | trans-gene identifier |
ncond | number of conditions required for mediation |
prob_med | probability of mediation in at least ncond conditions
|
The main element of interest for inference is the column prob_med.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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