inst/investigate_final_data.md

In philliplab/MotifBinner: Bin reads by Motif

Quick summary of final dataset obtained

Number of sequences

## [1] 3336

Number of ambiguity characters

## non_acgt
##    0    1    2    3    4    5    6    7    8    9   10   11 
## 2313  577  192   58   31   29   34   28   27   26   17    4

Outlying sequences

PCA of dist matrix

Top most outlying sequences

normal_ranks <- rank(tot_dist)
normal_ranks <- normal_ranks[order(normal_ranks)]

rank_comp <- data.frame(seq_name = names(normal_ranks),
           normal_rank = normal_ranks,
           normal_dist = tot_dist[match(names(normal_ranks),
                                        names(tot_dist))])
row.names(rank_comp) <- 1:nrow(rank_comp)
kable(head(rank_comp, 25))

|seq_name | normal_rank| normal_dist| |:------------|-----------:|-----------:| |CCTACCGCT_37 | 25| 87682.33| |TCCCGCTTG_18 | 25| 87682.33| |CTCCCCAAA_28 | 25| 87682.33| |CACACCGAT_13 | 25| 87682.33| |CATCTTGTC_21 | 25| 87682.33| |ACTGAATGT_50 | 25| 87682.33| |ATTCGTATG_23 | 25| 87682.33| |ACTTAGCCT_9 | 25| 87682.33| |TTTAACTTC_27 | 25| 87682.33| |AAAAAACCA_23 | 25| 87682.33| |TGTAGCTAC_15 | 25| 87682.33| |CAAACTATT_20 | 25| 87682.33| |CCCAAACAA_32 | 25| 87682.33| |ACTATTTGA_29 | 25| 87682.33| |CTGGCAGTC_36 | 25| 87682.33| |GGGTAGCTA_29 | 25| 87682.33| |GTTTAAAAT_16 | 25| 87682.33| |GAACAAAAG_6 | 25| 87682.33| |CGCGGCGGC_7 | 25| 87682.33| |AACGCCAGA_20 | 25| 87682.33| |CACCCCCCC_18 | 25| 87682.33| |TCCTGAGCC_35 | 25| 87682.33| |TGAGTCAAC_16 | 25| 87682.33| |GAATGCTCA_40 | 25| 87682.33| |CCCGTTATA_3 | 25| 87682.33|

kable(tail(rank_comp, 25))

| |seq_name | normal_rank| normal_dist| |:----|:------------|-----------:|-----------:| |3312 |ACCCTGCCA_2 | 3312| 344489.0| |3313 |CCACATTAA_2 | 3313| 344799.8| |3314 |TCGCGGCAA_2 | 3314| 345355.6| |3315 |CTGCGAAAC_25 | 3316| 345378.5| |3316 |ACTGAATAA_22 | 3316| 345378.5| |3317 |ACAAATCAC_25 | 3316| 345378.5| |3318 |GCGGCTGGA_2 | 3318| 345534.2| |3319 |GTTGGCTCG_5 | 3320| 345551.9| |3320 |GAAAATAAA_12 | 3320| 345551.9| |3321 |CAGATGTAC_23 | 3320| 345551.9| |3322 |AACATGGCA_3 | 3322| 347061.9| |3323 |GGTAGCCGG_18 | 3323| 348911.8| |3324 |CATAAATCC_4 | 3324| 349450.2| |3325 |GGAACTAAA_19 | 3325| 352077.0| |3326 |CACTCACAT_10 | 3326| 352385.6| |3327 |AACCCTAAA_5 | 3327| 356009.8| |3328 |TATAACTTA_20 | 3328| 356285.1| |3329 |TAGAAGTTG_20 | 3329| 360528.9| |3330 |AGCCAGGAA_22 | 3330| 360749.3| |3331 |GCCGAATTT_23 | 3331| 363638.1| |3332 |TAGCACTGC_2 | 3332| 395148.7| |3333 |CCGTTCCCA_19 | 3333| 600638.0| |3334 |AGATCATAC_28 | 3334| 805027.7| |3335 |CTGACGCCC_2 | 3335| 887888.7| |3336 |TGATGCTTC_16 | 3336| 2061046.6|

philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.