importMatrix of MEME file without w= and nsites= values in letter-probability string crashes

[Julie-Cardin]

Hello,

the MEME version we use doesn't genertare the w= and nsites= so

mportMatrix(..., format="meme") Error in (mat.fr + 1):(mat.fr + as.numeric(w)) : NA/NaN argument In addition: Warning message: In FUN(X[[i]], ...) : NAs introduced by coercion

does not work. Per the MEME standard, the length could be can be derived from the matrix if they are not specified, provided there is an empty line following the letter probability matrix [https://meme-suite.org/meme/meme_5.5.4/doc/meme-format.html]
and the nsites default to 20 if not specified....

Is this voluntary that your implementation needs w= and nsites= to work ?

What we have as data:

ALPHABET= ACGU

strands: +

MOTIF group0 group0

letter-probability matrix: alength= 4
0.2423856687440365	0.2423856687440365	0.27284299376789045	0.2423856687440365
0.22685969217988056	0.22685969217988056	0.3194209234603583	0.22685969217988056
0.21926418154603855	0.34220745536188435	0.21926418154603855	0.21926418154603855
0.2116735308861708	0.2116735308861708	0.36497940734148765	0.2116735308861708
0.20400140355966154	0.3879957893210154	0.20400140355966154	0.20400140355966154
0.19624139432687643	0.41127581701937077	0.19624139432687643	0.19624139432687643
0.1884194109033729	0.1884194109033729	0.1884194109033729	0.43474176728988123
0.17289070590064243	0.17289070590064243	0.48132788229807266	0.17289070590064243
0.1651631759627908	0.1651631759627908	0.1651631759627908	0.5045104721116277
0.5046694234925583	0.16511019216914724	0.16511019216914724	0.16511019216914724
0.17231399749328336	0.14126798752631473	0.5451500274540871	0.14126798752631473
0.11638505693861528	0.14527656898549268	0.11638505693861528	0.6219533171372769
0.0847707907081765	0.7456876278754705	0.0847707907081765	0.0847707907081765
0.05277970708083049	0.8109948507705643	0.08344573506777464	0.05277970708083049
0.022012491592590694	0.8741967112188684	0.022012491592590694	0.08177830559595012
0.8744016653645654	0.08170998754738446	0.02194417354402503	0.02194417354402503
0.01448287640318191	0.01448287640318191	0.8967855567870948	0.07424869040654133
0.0	1.0	0.0	0.0
0.001445661444688523	0.001445661444688523	0.001445661444688523	0.9956630156659344
0.794535180236837	0.16826237019703663	0.01860122478306317	0.01860122478306317
0.02622808218529049	0.9213157534441285	0.02622808218529049	0.02622808218529049
0.04948716677801554	0.04948716677801554	0.04948716677801554	0.8515384996659534
0.11133056406688091	0.6973952980662635	0.08117797469100574	0.11009616317584983
0.12750647131948215	0.09735388194360697	0.6777857647933039	0.09735388194360697
0.15026844489399413	0.12011585551811896	0.609499844069768	0.12011585551811896
0.15032502939641434	0.15032502939641434	0.5490249118107569	0.15032502939641434
0.45926561782286185	0.18024479405904603	0.18024479405904603	0.18024479405904603
0.2034975511030523	0.2034975511030523	0.3895073466908431	0.2034975511030523
0.22683171378041145	0.22683171378041145	0.3195048586587657	0.22683171378041145
0.242316306685997	0.27305107994200906	0.242316306685997	0.242316306685997```

Thanks.

[jianhong]

Hi,

Thank you for reporting this. This should be fixed in the development version. Let me know if it does not work for you.
To indstall the development version:
BiocManager::install('jianhong/motifStack')

Jianhong.

[Julie-Cardin]

Hi,
Your fix in dev version work perfectly well for me!
MANY THANKS for this very fast and efficient answer!
:)