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Set up the polynomial design

Source: R/sc.set.poly.R
sc.set.poly.Rd

sc.set.poly() builds the design of the maSigPro model (Conesa et al. 2006): a 0/1 dummy for every path but the first, the reference, and the products of each dummy with each power of the binned pseudotime up to poly_degree.

The reference is reference when it is given. Otherwise it is the first path of the Dense slot: after sc.squeeze(), the first level of a factor path column, or else the first label in C-locale (byte) order; after sc.restruct(), the first path of end_node_list; with bins given to create_scmp() or cDense(), the path of the first bin. The other paths keep the order of the Dense slot.

Usage

sc.set.poly(
  scmpObj,
  poly_degree = 2,
  bin_ptime_col = scmpObj@Parameters@bin_ptime_col,
  path_col = scmpObj@Parameters@path_col,
  reference = NULL
)

Arguments

scmpObj

A ScMaSigPro object.

poly_degree

The degree of the polynomial in pseudotime.

bin_ptime_col

The name of the column of the bin metadata that holds the binned pseudotime of each bin.

path_col

The name of the column of the cell or bin metadata that holds the path label of each cell or bin.

reference

The reference path, one of the path labels of the Dense slot, or NULL for the first path.

Value

The object with the design in the Design slot (class MatrixDesign).

References

Conesa A, Nueda MJ, Ferrer A, Talón M (2006). maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22(9), 1096-1102. doi:10.1093/bioinformatics/btl056

Srivastava P, Benegas Coll M, Götz S, Nueda MJ, Conesa A (2024). scMaSigPro: differential expression analysis along single-cell trajectories. Bioinformatics 40(7), btae443. doi:10.1093/bioinformatics/btae443

See also

showPoly(), predictors() and pathAssign(), which read the design; MatrixDesign.

Other workflow steps: sc.cluster.trend(), sc.filter(), sc.p.vector(), sc.restruct(), sc.squeeze(), sc.t.fit()

Author

Priyansh Srivastava spriyansh29@gmail.com, Ana Conesa and Maria Jose Nueda, mj.nueda@ua.es

Examples

data("scmp.ob", package = "scMaSigPro")
scmp <- sc.set.poly(scmp.ob, poly_degree = 2)
showPoly(scmp)
#> [1] "beta0 + beta1*Path2vsPath1 + beta2*scmp_binned_pseudotime + beta3*scmp_binned_pseudotimexPath2 + beta4*scmp_binned_pseudotime2 + beta5*scmp_binned_pseudotime2xPath2"