Testing for Cell Type-Specific Gene Expression Differences

Uses csSAM (Shen-Orr et al. (2010)) to estimate cell type-specific expression and test for group differences in each cell type.

bseqsc_csdiff(formula, data = NULL, ...)

Arguments

formula

csSAM model to fit specified as a formula

data

cell type proportion matrix (samples x cell types).

...

other arguments passed to csSAM::csSAMfit.

References

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). “Cell type-specific gene expression differences in complex tissues.” Nature methods, 7(4), pp. 287-9. ISSN 1548-7105, doi: 10.1038/nmeth.1439 (URL: http://doi.org/10.1038/nmeth.1439).