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@cristinapasi-14734
Last seen 3.8 years ago

Hello,

I have tried to use the get_link function for an application I am developing in Shiny, however the link redirects to a page where of the list of proteins that I have passed as STRING_id, it only recognises the first one as the following ones are all preceded by "0D".  I believe it must be some issue on how the link is created and how the list of STRING_ids are then separated when the string-db.org webpage opens.

I hope you can help me with this,

Best regards,

Cristina

STRINGdb get_link bug • 658 views
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Dear Cristina,

can you paste the call you are making? (including the input)

Best, Damian.

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Hi Damian!

Thanks for your reply!  If I use the internal example to the STRINGdb package everything works however this is the dataset of differentially expressed proteins I have:

> tomap

p-value   LogFC protein

1  0.0000  3.3334 YBR117C

2  0.0003 -0.5578 YBR249C

3  0.0026  0.5085 YCL040W

4  0.0043 -0.4235 YGL148W

5  0.0000  2.0330 YGR043C

6  0.0000  1.1019 YGR248W

7  0.0000  0.9537 YMR105C

8  0.0000  2.4107 YMR169C

And this is the code I am using:

> string_db <- STRINGdb$new( version="10", species=4932, score_threshold=0, input_directory="" ) > example1_mapped <- string_db$map(tomap, "protein", removeUnmappedRows = TRUE )
> hits <- example1_mapped$STRING_id[1:10] > link1 <- string_db$get_link(hits)

And this is the link I get:  http://version10.string-db.org/10/p/8078305016

It should stay valid for a while so you can see what I mean.

Cristina

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Hi Cristina,

The attached simple example of parsing a list of names to the get_link function seems to work. From the example you have provided it seems that you are slicing the example1_mapped vector with indices ([1:10]) which are larger than the vector length (8). This results in "NA" being appended to the vector (hence the error in the link you have attached).

> a <- c("YBR117C", "YBR249C")
> m <- data.frame(a)
> d <- string_db$map(m, "a", removeUnmappedRows = TRUE ) > h <- d$STRING_id[1:2]
> h
[1] "4932.YBR117C" "4932.YBR249C"
>  string_db\$get_link(h)

I get: http://version10.string-db.org/10/p/8219305039 which is correct.

Best,

Damian.

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You are right, thank you very much!