Creates the design matrix used by the edgeR/limma based
methods (find_camera_hit, find_roast_hit,
compute_barcode_statistics, filter_by_variance
and plot_barcode_hit) from the groups of the ScreenR
object. The matrix has no intercept: it has one column for each group,
so that each coefficient is the mean of a group and a comparison
between groups is expressed with a contrast created by
create_contrast. The column names are syntactically valid
versions of the group names (for example "T1/T2" becomes "T1.T2").
Row names are sample identifiers in the order of the object. All
model-based ScreenR functions check that this order matches the
object. Recreate the design after subsetting or reordering samples.
For a custom design from model.matrix(), explicitly set its row names
to the identifiers of the samples used to construct its rows; unnamed
rows or default numeric row names do not establish sample alignment.
Named contrast vectors are aligned to the design columns; unnamed
vectors are interpreted in column order.
Arguments
- screenR_Object
The ScreenR object obtained using
create_screenr_object.
Examples
object <- get0("object", envir = asNamespace("ScreenR"))
create_design_matrix(object)
#> Control T1.T2 Treated
#> T1 0 1 0
#> T2 0 1 0
#> Time3_TRT_A 0 0 1
#> Time3_TRT_B 0 0 1
#> Time3_TRT_C 0 0 1
#> Time3_A 1 0 0
#> Time3_B 1 0 0
#> Time3_C 1 0 0
#> Time4_TRT_A 0 0 1
#> Time4_TRT_B 0 0 1
#> Time4_TRT_C 0 0 1
#> Time4_A 1 0 0
#> Time4_B 1 0 0
#> Time4_c 1 0 0
#> attr(,"assign")
#> [1] 1 1 1
#> attr(,"contrasts")
#> attr(,"contrasts")$groups
#> [1] "contr.treatment"
#>