9.3 Assess the quality of networks
9.3.1 Introduction to the network file by SJARACNe
The core output of SJARACNe is the network file named consensus_network_ncol_.txt. It contains 9 columns:
- source: ID of the source gene, can be the gene symbol;
- target: ID of the target gene, can be the gene symbol;
- source.symbol: symbol of the source gene;
- target.symbol: symbol of the target gene;
- MI: mutual information of source-gene pair;
- pearson: Pearson correlation coefficient, [-1,1]
- pearson: Spearman correlation coefficient, [-1,1]
- slope: slop of the regression line, returned by
stats.linregression() - p.value: p-value for a hypothesis test whose null hypothesis is that the slope is zero, using Wald Test with t-distribution of the test statistic
network_format <- read.table(system.file("extdata/demo_pbmc14k/PBMC14k/SJARACNe/B/TF/bt100_pc001/consensus_network_ncol_.txt", package = "scMINER"),
header = T, sep = "\t", quote = "", stringsAsFactors = F)
head(network_format)## source target source.symbol target.symbol MI pearson spearman slope
## 1 AATF ACBD3 AATF ACBD3 0.0509 -0.0310 -0.0311 -0.0193
## 2 AATF ADD3 AATF ADD3 0.0486 0.0228 0.0258 0.0307
## 3 AATF AES AATF AES 0.0511 0.0311 0.0289 0.0668
## 4 AATF AKR7A2 AATF AKR7A2 0.0498 0.0319 0.0366 0.0421
## 5 AATF AL928768.3 AATF AL928768.3 0.0447 0.0247 0.0293 0.0335
## 6 AATF ALG8 AATF ALG8 0.0479 0.0358 0.0373 0.0234
## p.value
## 1 0.1761
## 2 0.3204
## 3 0.1756
## 4 0.1646
## 5 0.2815
## 6 0.11839.3.2 Generate network QC report
There is no simple standards to tell the reliability of networks. Empirically, a network with 50-300 target size is good. scMINER provides a function, drawNetworkQC(), to quickly assess the quality of networks in batch.
network_stats <- drawNetworkQC(sjaracne_dir = "/work-path/PBMC14K/SJARACNe", generate_html = FALSE) # Set `generate_html = TRUE` to generate html-format QC report for each network file## The network QC statistics table is saved seperately, for demonstration purposes.
network_stats <- readRDS(system.file("extdata/demo_pbmc14k/PBMC14k/SJARACNe/network_stats.rds", package = "scMINER"))
head(network_stats)## network_tag network_node network_edge driver_count targetSize_mean
## 1 B.SIG.bt100_pc001 8572 391889 4148 94.47662
## 2 B.TF.bt100_pc001 8572 95341 835 114.18084
## 3 CD4TCM.SIG.bt100_pc001 8660 382153 4209 90.79425
## 4 CD4TCM.TF.bt100_pc001 8660 94319 838 112.55251
## 5 CD4TN.SIG.bt100_pc001 8612 401658 4180 96.09043
## 6 CD4TN.TF.bt100_pc001 8612 95152 831 114.50301
## targetSize_median targetSize_minimum targetSize_maximum
## 1 94.0 33 396
## 2 96.0 64 913
## 3 91.0 31 281
## 4 95.5 60 689
## 5 95.0 43 303
## 6 99.0 64 743
## network_path
## 1 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/B/SIG/bt100_pc001/sjaracne_workflow-df798096-8dee-4baf-8f70-891c689dc769/consensus_network_ncol_.txt
## 2 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/B/TF/bt100_pc001/sjaracne_workflow-fb2a69b9-f98e-47ff-87a0-6d538822fc6e/consensus_network_ncol_.txt
## 3 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/CD4TCM/SIG/bt100_pc001/sjaracne_workflow-424f1068-13d1-4f0e-9c26-56acd9a2027c/consensus_network_ncol_.txt
## 4 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/CD4TCM/TF/bt100_pc001/sjaracne_workflow-52b3cdf5-5914-4c8c-a77a-05f17c755d83/consensus_network_ncol_.txt
## 5 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/CD4TN/SIG/bt100_pc001/sjaracne_workflow-7b5bb68e-1de5-4d0e-80ec-8d8aa037866f/consensus_network_ncol_.txt
## 6 /Volumes/projects/scRNASeq/yu3grp/scMINER/NG_Revision/QPan/scminer_R/Datasets/PBMC14K/SJARACNe/CD4TN/TF/bt100_pc001/sjaracne_workflow-89716541-eb53-435c-8a45-bab63d6b5198/consensus_network_ncol_.txt