correlateTrajectories.Rd
This function will correlate 2 trajectory matrices from getTrajectory.
correlateTrajectories( seTrajectory1 = NULL, seTrajectory2 = NULL, corCutOff = 0.5, varCutOff1 = 0.8, varCutOff2 = 0.8, removeFromName1 = c("underscore", "dash"), removeFromName2 = c("underscore", "dash"), useRanges = FALSE, fix1 = "center", fix2 = "start", maxDist = 250000, log2Norm1 = TRUE, log2Norm2 = TRUE, force = FALSE, logFile = createLogFile("correlateTrajectories") )
seTrajectory1 | A |
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seTrajectory2 | A |
corCutOff | A numeric describing the cutoff for determining correlated features. |
varCutOff1 | The "Variance Quantile Cutoff" to be used for identifying the top variable features across |
varCutOff2 | The "Variance Quantile Cutoff" to be used for identifying the top variable features across |
removeFromName1 | A character vector describing how to filter names in matrix 1. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept. |
removeFromName2 | A character vector describing how to filter names in matrix 2. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept. |
useRanges | A boolean describing whether to use range overlap matching for correlation analysis. |
fix1 | A character describing where to resize the coordinates of |
fix2 | A character describing where to resize the coordinates of |
maxDist | A integer specifying the maximum distance between the coordinates of |
log2Norm1 | A boolean describing whether to log2 normalize |
log2Norm2 | A boolean describing whether to log2 normalize |
force | A boolean value that determines whether analysis should continue if resizing coordinates in |
logFile | The path to a file to be used for logging ArchR output. |