Hi Tamas: Yes. It confused me for a while, but I am clear about it now. Thanks
Best Quanwei On 12/17/13 6:20 PM, "Tamás Nepusz" <[email protected]> wrote: >> >> gene pair. So I firstly mapped the genes into ids (from 1 to n, where n >>is the gene number) and then describe the network by ids. Finally I used >>"read.graph(file="biggestComponent_id.txt",format="edge list") to input >>the network. But I found the ids seems different from the input ids >>(likely added by "1"). >Most of igraph is written in C, which uses zero-based indices by default >(so edge and vertex IDs start from zero). However, R is using 1-based >indices everywhere so the R interface of igraph also provides 1-based >indexing almost everywhere; the only exception is the edgelist file >format. This is because edge list files may be saved and loaded from the >C core of igraph or from the Python interface of igraph as well, so there >would be quite a bit of confusion if edge lists saved from R used 1-based >indices while edge lists saved from C or Python used 0-based indices. >Therefore, whenever you load an edge list into igraph¹s R interface, >igraph assumes that the vertex indices in the file are 0-based and adds 1 >to them automatically to obtain the vertex IDs that R will use. >Similarly, whenever you save an edge list from igraph¹s R interface into >a file, igraph will subtract 1 from the vertex IDs used in R to obtain a >0-based indexing. > >Best, >T. > > > >_______________________________________________ >igraph-help mailing list >[email protected] >https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
