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