sqjin
inferRegulations function example
Thank you for your great work! I wonder if there is any examples in using the inferRegulations() function. I noticed that the A549 dataset was used to evaluated the reconstructed GRN. However, there exists no detailed usages in the example Walkthrough.
I tried to use this function after the scAI object is created.
My pipeline is as follows:
load("/home/zwh/program/scAI-master/data/data_A549.rda")
X <- data_A549$data # List of data matrix
labels <- data_A549$labels # the collected time of cells, which is used for validation
scAI_outs <- create_scAIobject(raw.data = X)
scAI_outs <- preprocessing(scAI_outs, assay = NULL, minFeatures = 200, minCells = 1,
libararyflag = F, logNormalize = F)
scAI_outs <- addpData(scAI_outs, pdata = labels, pdata.name = "Time")
scAI_outs <- run_scAI(scAI_outs, K = 5, nrun = 32)
markers_ATAC <- identifyFactorMarkers(scAI_outs, assay = 'ATAC', n.top = 5)
gene.use = c('GPR153','ACOT7')
scAI_GRN <- inferRegulations(scAI_outs,gene.use = gene.use ,candinate_loci = markers_ATAC)
However, the returned scAI_GRN has Null values. In addition, how to directly get the TF-GENE regulatory inference results. In scAI_GRN, I noticed that the results are presented in the TF-factor-loci format. But in the published paper, the reconstructed GRN on A549 dataset was shown in the TF-gene level. Thank you in advance. Scotty Zhang
