Pick power to fit network to a scale-free topology
Arguments
- exp
A gene expression data frame with genes in row names and samples in column names or a `SummarizedExperiment` object.
- net_type
Network type. One of 'signed', 'signed hybrid' or 'unsigned'. Default is signed.
- rsquared
R squared cutoff. Default is 0.8.
- cor_method
Correlation method. One of "pearson", "biweight" or "spearman". Default is "spearman".
Value
A list containing:
powerOptimal power based on scale-free topology fit
plotA ggplot object displaying main statistics of the SFT fit test
Examples
data(filt.se)
sft <- SFT_fit(filt.se, cor_method = "pearson")
#> Warning: executing %dopar% sequentially: no parallel backend registered
#> Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
#> 1 3 0.3340 1.0300 0.18900 145.0 149.0 222.0
#> 2 4 0.2060 0.5420 0.05910 116.0 114.0 195.0
#> 3 5 0.1460 0.3930 -0.00703 96.8 91.3 176.0
#> 4 6 0.0556 0.1930 -0.07170 83.6 74.2 162.0
#> 5 7 0.0209 0.1050 -0.07690 73.7 61.8 151.0
#> 6 8 0.0015 -0.0255 -0.12100 66.0 51.9 142.0
#> 7 9 0.0443 -0.1400 -0.16000 59.8 46.5 134.0
#> 8 10 0.1470 -0.2570 -0.08480 54.7 43.2 127.0
#> 9 11 0.2570 -0.3460 0.04810 50.4 39.7 121.0
#> 10 12 0.3320 -0.3770 0.14800 46.7 36.6 116.0
#> 11 13 0.4520 -0.4400 0.29700 43.5 32.8 111.0
#> 12 14 0.5470 -0.4910 0.41800 40.8 30.1 107.0
#> 13 15 0.5880 -0.5240 0.47300 38.3 27.6 103.0
#> 14 16 0.6870 -0.5470 0.59800 36.1 24.8 99.5
#> 15 17 0.7570 -0.5730 0.68900 34.1 22.9 96.1
#> 16 18 0.8060 -0.5880 0.75100 32.3 21.4 93.0
#> 17 19 0.8350 -0.6170 0.78800 30.7 20.1 90.1
#> 18 20 0.8770 -0.6480 0.84100 29.2 19.3 87.4