Re: [igraph] Adjacency list to edgelist

[Gábor Csárdi]

You might have a different file format than I used, e.g. tabulators
instead of spaces. (This is why it is better to attach an example
file, than putting it into the mail.)

Gábor

On Tue, Mar 9, 2010 at 6:07 PM, anupam sinha <address@hidden> wrote:
> Hi Gabor,
>                    Tried your code but it is giving an empty edgelist
> object. Any suggestions ?
>
> Regards,
>
> Anupam
>
> On Tue, Mar 9, 2010 at 10:15 PM, anupam sinha <address@hidden>
> wrote:
>>
>> Dear Gabor,
>>
>>                          Thanks a lot for your reply.
>>
>> Regards,
>>
>> Anupam
>>
>>
>> On Tue, Mar 9, 2010 at 6:22 PM, Gábor Csárdi <address@hidden> wrote:
>>>
>>> Dear Anupam,
>>>
>>> you don't really need igraph for this:
>>>
>>> lines <- readLines("adjlist.txt")
>>> lines <- gsub("[ ]+$", "", gsub("[ ]+", " ", lines))   # remove
>>> trailing and multiple spaces
>>> adjlist <- strsplit(lines, " ")
>>>
>>> col1 <- unlist(lapply(adjlist, function(x) rep(x[1], length(x)-1)))
>>> col2 <- unlist(lapply(adjlist, "[", -1))
>>>
>>> edgelist <- cbind(col1, col2)
>>>
>>> Best,
>>> Gabor
>>>
>>> On Tue, Mar 9, 2010 at 1:39 PM, anupam sinha <address@hidden>
>>> wrote:
>>> > Dear all,
>>> >
>>> >                    I have a number of graphs in this format (adjacency
>>> > list)
>>> > :
>>> >
>>> > PABPC4    PABPC4    EEF1A1    SETDB1    XRN1    RIF1
>>> > AHCY         AHCY
>>> > PSCDBP   PSCDBP    PSCD1
>>> > ITSN2        ITSN2    WAS    RAD9A    LSM8    SYNJ2
>>> > TICAM2     TICAM2    IL1R1    IRAK1    TRAF6    IRF3    TLR4    IL1RAP
>>> > IRAK3    IRF7    TIRAP
>>> > ADCY3      CAMK2G    ADCY3
>>> > ADCY6      ADCY6    CHRNA7    GNAS    RAF1
>>> > FHL3          FHL3    ACTB    CDC25B    MAPK1    LASP1    KLF8    CTBP2
>>> > FHL2    ZNF42    SRF    CDC42EP1    PHC2    PCQAP
>>> > TM9SF2    TM9SF2    RAB9A
>>> >
>>> > where the alphanumeric id represents the node name (gene name). The
>>> > first
>>> > column contains the source node and the other columns have the
>>> > destination
>>> > nodes. How do I convert this into an edgelist format using R
>>> > implementation
>>> > of igraph ? Thanks in advance for any suggestions.
>>> >
>>> >
>>> > Regards,
>>> >
>>> >
>>> > Anupam
>>> >
>>> > _______________________________________________
>>> > igraph-help mailing list
>>> > address@hidden
>>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Gabor Csardi <address@hidden>     UNIL DGM
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>>
>> --
>> Graduate Student,
>> Laboratory of Computtational Biology,
>> Centre For DNA Fingerprinting And Diagnostics,
>> 4-1-714 to 725/2, Tuljaguda complex
>> Mozamzahi Road, Nampally,
>> Hyderabad-500001
>
>
>
> --
> Graduate Student,
> Laboratory of Computtational Biology,
> Centre For DNA Fingerprinting And Diagnostics,
> 4-1-714 to 725/2, Tuljaguda complex
> Mozamzahi Road, Nampally,
> Hyderabad-500001
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM