I have a gold standard in Arabidopsis thaliana( genes and transcription factors and their interaction) like below
TFLocus TargetLocus InteractionType AT5G10140 AT1G65480 -1 AT5G11260 AT1G27480 -1 AT5G11260 AT5G53370 -1 AT5G11260 AT1G03630 -1 AT5G11260 AT1G13600 -1 AT5G11260 AT2G41670 -1 AT5G11260 AT2G05160 -1 AT5G11260 AT2G40170 -1 AT5G11260 AT1G62780 -1
I want to convert this data frame to graph by igraph package, I did like so
mycounts <- read.table("Ara_GoldST.txt", header = T, sep = "\t") mycounts <- graph.data.frame(mycounts, directed=TRUE, vertices=NULL) mycounts <- get.data.frame(mycounts, what=c("edges", "vertices", "both"))
Then I want to convert the graph to adjacency matrix but
> get.adjacency(mycounts, type=c("both", "upper", "lower"), + attr=NULL, names=TRUE, binary=FALSE, sparse=FALSE) Error in get.adjacency(mycounts, type = c("both", "upper", "lower"), attr = NULL, : unused argument (binary = FALSE)
How I can convert my data frame to a graph that can be converted to an adjacency matrix please?