sim_score_grp: Summary Scores by Groups of Cell Types

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Description

Function appends two columns (score_column_grp1, score_column_grp2) to GESS result tibble. The appended columns contain cell-summarized scores for groups of cell types, such as normal and tumor cells. The cell-summarized score is obtained the same way as the NCSct scores, that is using a maximum quantile statistic. It compares the 67 and 33 quantiles of scores and retains whichever is of higher absolute magnitude.

Usage

sim_score_grp(tib, grp1, grp2, score_column)

Arguments

tib	tibble in gessResult object
grp1	character vector, group 1 of cell types, e.g., tumor cell types
grp2	character vector, group 2 of cell types, e.g., normal cell types
score_column	character, column name of similarity scores to be grouped

Value

tibble

Examples

gr <- gessResult(result=dplyr::tibble(pert=c("p1", "p1", "p2", "p3"),
                                      cell=c("MCF7", "SKB", "MCF7", "SKB"),
                                      type=rep("trt_cp", 4),
                                      NCS=c(1.2, 1, 0.9, 0.6)),
                 query=list(up="a", down="b"), 
                 gess_method="LINCS", refdb="path/to/refdb")
df <- sim_score_grp(result(gr), grp1="SKB", grp2="MCF7", "NCS")

signatureSearch documentation built on April 16, 2021, 6 p.m.