Annotate NMF factors with Bagaev et al. (2021) MFP subtypes
map_factors_to_TME.RdFor a single cancer type, matches TCGA patients present in the NMF factor
score matrix Z to the Bagaev et al. (2021) MFP annotation shipped with the
package, then tests each factor across the four MFP subtypes (IE, IE/F, F, D)
with a Kruskal-Wallis test. Factors with p < 0.05 are labelled with the subtype
that has the highest median factor score; the others are labelled
"uncharacterized".
Arguments
- cancer_name
Character. Cancer type abbreviation matching the
TCGA_projectcolumn of the internal annotation (case-insensitive, e.g."skcm").- Z
Numeric matrix. Samples x factors NMF score matrix (row names = TCGA barcodes).
- plot
Logical. If TRUE (default), saves violin/boxplots of factor scores by MFP group to
Results/TME_factors_MFP_<cancer_name>_<file_name>.pdf.- file_name
Optional character suffix for saving output plots.