Get_p2g_fun: Filter peak-to-gene link
In jiang-junyao/IReNA: IReNA
Get_p2g_fun R Documentation
Filter peak-to-gene link
Description
Extract peak to gene links data.frame from ArchR object, then identify
significant links based on corCutOff, FDRCutOff, varCutOffATAC and varCutOffRNA.
Usage
Get_p2g_fun(
ArchR_obj,
corCutOff = 0.2,
FDRCutOff = 1e-06,
varCutOffATAC = 0.7,
varCutOffRNA = 0.3
)
Arguments
ArchR_obj
ArchR object with Peak2GeneLinks information in peakset slot
corCutOff
numeric, correlation between each peak and gene to refine p2g
FDRCutOff
numeric, FDR of peak to gene link to refine p2g
varCutOffATAC
numeric, VarQATAC to refine p2g
varCutOffRNA
numeric, VarQRNA to refine p2g
jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.
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| Get_p2g_fun | R Documentation |
Filter peak-to-gene link
Description
Extract peak to gene links data.frame from ArchR object, then identify significant links based on corCutOff, FDRCutOff, varCutOffATAC and varCutOffRNA.
Usage
Get_p2g_fun(
ArchR_obj,
corCutOff = 0.2,
FDRCutOff = 1e-06,
varCutOffATAC = 0.7,
varCutOffRNA = 0.3
)
Arguments
ArchR_obj |
ArchR object with Peak2GeneLinks information in peakset slot |
corCutOff |
numeric, correlation between each peak and gene to refine p2g |
FDRCutOff |
numeric, FDR of peak to gene link to refine p2g |
varCutOffATAC |
numeric, VarQATAC to refine p2g |
varCutOffRNA |
numeric, VarQRNA to refine p2g |
R Package Documentation
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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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