Create a group effect object to detect a shift in usage of features which are ordered within a group.

group_effect_shift(design, coef1, coef2, design_common = NULL)

group_effect_shift_stepup(design, coef1, coef2, design_common = NULL)

group_effect_shift_stepdown(design, coef1, coef2, design_common = NULL)

group_effect_shift_log2(design, coef1, coef2, design_common = NULL)

group_effect_shift_stepup_log2(design, coef1, coef2, design_common = NULL)

group_effect_shift_stepdown_log2(design, coef1, coef2, design_common = NULL)

Arguments

design

Design matrix.

coef1

Column number of coefficient for first condition in design matrix.

coef2

Column number of coefficient for second condition in design matrix.

design_common

Experimental! Optional sample-level design matrix. For example, this can be used to account for a batch effect or matched samples.

Value

A group effect object.

Details

group_effect_shift_log2 is almost certainly the version you want.

The coefficients should represent the expression levels in two different conditions.

The _stepup and _stepdown versions may be used to look for shifts in start or end of transcription from RNA-seq or microarray data, where the observed levels are expected to be cumulative or reverse cumulative.

See also

effect_shift, effect_shift_log2