get_mean_median: Extract mean and median correlation coefficient values

In scFeatureFilter: A correlation-based method for quality filtering of single-cell RNAseq data

Description

Takes the output of correlate_windows and extract the mean and the median correlation value for each window comparison.

Usage

get_mean_median(df, absolute_cc = TRUE)

Arguments

df	A data frame, usually the output of correlate_windows.
absolute_cc	Should the function work of absolute value of correlation coefficients? Default to TRUE to simplify plots and avoid annoying, non-symmetrical, near 0, shifts of distributions.

Value

A data_frame with columns bin, window, mean and median.

Examples

library(magrittr)
expMat <- matrix(
    c(1, 1, 5,
      1, 2, 3,
      0, 1, 4,
      0, 0, 2),
    ncol = 3, byrow = TRUE, dimnames = list(paste("gene", 1:4), paste("cell", 1:3))
)

calculate_cvs(expMat) %>%
    define_top_genes(window_size = 2) %>%
    bin_scdata(window_number = 1) %>%
    correlate_windows(n_random = 2) %>%
    get_mean_median

scFeatureFilter documentation built on Nov. 8, 2020, 7:49 p.m.