oligoSummary not populating the motif matrix output field

[jesswhitts]

Hello,

I'm trying to run oligoSummary, in order to use motifStack as shown in the vignette, but for some reason when I run it the $motif section is not being populated, and just says NA. The other sections are being filled.

Code:

summary of the short oligos

freqs <- oligoFrequency(Hsapiens$chr1, MarkovOrder=3) os <- oligoSummary(seq, oligoLength=6, MarkovOrder=3, quickMotif=FALSE, freqs=freqs)

freqs A C G T AAA AAC AAG AAT ACA 0.2630721269 0.1886631689 0.1886316745 0.2634647638 0.0334716679 0.0128935366 0.0179881397 0.0215514929 0.0178128784 ACC ACG ACT AGA AGC AGG AGT ATA ATC 0.0107751226 0.0022441549 0.0145656929 0.0200149752 0.0130548281 0.0167887847 0.0145635986 0.0176340383 0.0119421488 ....etc

seq GRanges object with 8029 ranges and 5 metadata columns: seqnames ranges strand | peakNames score upstream downstream

| [1] chr1 180700-181906 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 178.0 20 20 [2] chr1 909801-910737 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 54.5 20 20 [3] chr1 923791-925753 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 49.0 20 20 [4] chr1 928875-929592 * | gr1__sig_R1_pea..,gr2__sig_R2_pea.. 40.5 20 20 [5] chr1 939838-943041 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 23.5 20 20 ... ... ... ... . ... ... ... ... [8025] chrX 153672778-153674038 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 24.5 20 20 [8026] chrX 153689045-153689654 * | gr1__sig_R1_pea..,gr2__sig_R2_pea.. 34.5 20 20 [8027] chrX 153879164-153879902 * | gr1__sig_R1_pea..,gr2__sig_R2_pea.. 26.5 20 20 [8028] chrX 155026647-155027494 * | gr2__sig_R2_pea..,gr1__sig_R1_pea.. 112.0 20 20 [8029] chrY 4034003-4034678 * | gr1__sig_R1_pea..,gr2__sig_R2_pea.. 61.0 20 20 sequence [1] NNNNNNNNNNNNNNNNNNNN.. [2] TTGCCTCCCACAGGCTGACA.. [3] GCCTGACCAACATGGTGAAA.. [4] GTGCACAACGACACGATGTC.. [5] TGGGCGCAGAGCTGTTCCTG.. ... ... [8025] TCCGGCCCTGGAAGCCCTGG.. [8026] GGCACTGCTGTCGACGGCAA.. [8027] TTGTCTCCGAGCAACTTAAG.. [8028] AAATAACTCAAGTTTTTTTC.. [8029] TAATCCGTAAGGAACTTAAT.. ------- seqinfo: 24 sequences from an unspecified genome

os file I am getting:

os $zscore aaaaaa aaaaac aaaaag aaaaat aaaaca aaaacc aaaacg aaaact aaaaga -1.386023e+03 -6.786546e+01 -8.377371e+01 -1.091797e+02 -4.729527e+01 -3.655862e+01 -9.319195e+00 -4.210806e+01 -4.731548e+01 aaaagc aaaagg aaaagt aaaata aaaatc aaaatg aaaatt aaacaa aaacac -3.692042e+01 -5.187627e+01 -4.000877e+01 -4.078904e+01 -4.320826e+01 -4.690237e+01 -5.486493e+01 -1.205061e+01 -2.717602e+01 ...etc

$counts aaaaaa aaaaac aaaaag aaaaat aaaaca aaaacc aaaacg aaaact aaaaga aaaagc aaaagg aaaagt aaaata aaaatc aaaatg aaaatt aaacaa aaacac 4231 3063 3887 4702 3660 2429 688 2803 3782 2465 2726 2868 4509 2631 3666 4179 3327 2359 aaacag aaacat aaacca aaaccc aaaccg aaacct aaacga aaacgc aaacgg aaacgt aaacta aaactc aaactg aaactt aaagaa aaagac aaagag aaagat 2806 2703 2622 2578 415 2135 504 445 515 573 2015 2409 2553 2411 3972 2157 2909 2535 ...etc

$expCnt aaaaaa aaaaac aaaaag aaaaat aaaaca aaaacc aaaacg aaaact aaaaga aaaagc aaaagg 8021.51382 5789.99652 6687.38991 7376.03652 5605.44329 4066.77318 958.78499 4664.63641 5704.78352 4118.56570 4981.71410 aaaagt aaaata aaaatc aaaatg aaaatt aaacaa aaacac aaacag aaacat aaacca aaaccc 4638.68760 6076.86164 4549.56036 5597.14974 6229.18700 3866.52858 3569.03014 4436.17871 3611.63569 3316.70012 2987.08929 ...etc

$motifs [1] NA NB all of these sections are the same length (>3000 entries), I just shortened them for this post.

Any idea what might be causing this issue, and how I can fix it?

Many thanks, Jess

R version - 4.2.0 ChIPpeakAnno version - 3.32.0

[jianhong]

Did you tried to set quickMotif=TRUE for the function oligoSummary?

[jesswhitts]

ah it works now! Thanks so much :)