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## Re: [igraph] about vertex id (in R)

**From**: |
Qunawei Zhang |

**Subject**: |
Re: [igraph] about vertex id (in R) |

**Date**: |
Tue, 17 Dec 2013 19:57:44 -0500 |

**User-agent**: |
Microsoft-MacOutlook/14.3.8.130913 |

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" <address@hidden> 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.*
>
>
>
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