Performing Differential Expression¶
Firth Logistic Expression¶
After normalization, differential expression can be performed. Currently only Firth’s Logistic Regression is implemented. Firth Logistic Regression requires three values. A design which specifies condition and covariates of interest in this form
Without Covariates:
"Condition[VAR] ~ counts"
Alternatively covariates can be specified by adding them before counts
separated by a +
.
With Covariates:
"Codition[VAR] ~ COV1+COV2+COVN+counts"
Example:
detk-de firth "Codition[VAR] ~ COV1+COV2+COVN+counts" MyNormalizedCounts MyInfoFile -o MyDifferentialExpression
Note:
A tsv file is created when specifying output with -o