BASiCS_VarThresholdSearchHVG {BASiCS} | R Documentation |
Detection method for highly and lowly variable genes using a grid of variance contribution thresholds. Only used when HVG/LVG are found based on the variance decomposition.
BASiCS_VarThresholdSearchVG( Chain, Task = c("HVG", "LVG"), VarThresholdsGrid, EFDR = 0.1, Progress = TRUE ) BASiCS_VarThresholdSearchHVG(...) BASiCS_VarThresholdSearchLVG(...)
Chain |
an object of class |
Task |
See |
VarThresholdsGrid |
Grid of values for the variance contribution threshold (they must be contained in (0,1)) |
EFDR |
Target for expected false discovery rate related to
HVG/LVG detection. Default: |
Progress |
If |
... |
Passed to methods. |
See vignette
BASiCS_VarThresholdSearchHVG
A table displaying the results of highly variable genes detection for different variance contribution thresholds.
BASiCS_VarThresholdSearchLVG
A table displaying the results of lowly variable genes detection for different variance contribution thresholds.
Catalina A. Vallejos cnvallej@uc.cl
Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.
data(ChainSC) BASiCS_VarThresholdSearchHVG(ChainSC, VarThresholdsGrid = seq(0.55,0.65,by=0.01), EFDR = 0.10) BASiCS_VarThresholdSearchLVG(ChainSC, VarThresholdsGrid = seq(0.35,0.45,by=0.01), EFDR = 0.10)