dataset,PRJNA673886,PRJNA673886
[1] "2023-11-23 11:57:42 CST"
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: grid

Attaching package: ‘genomation’

The following objects are masked from ‘package:methylKit’:

    getFeatsWithTargetsStats, getFlanks, getMembers,
    getTargetAnnotationStats, plotTargetAnnotation

Warning message:
replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ 
[1] "dataset,PRJNA673886,PRJNA673886"
[1] "dataset"     "PRJNA673886" "PRJNA673886"
[1] 0 1 1 0
 num [1:4] 0 1 1 0
NULL
[[1]]
[1] "/home/xxia/public_html/django/fishcode/static/magicRversion1/data/vjnpdbLQYKuc0sqi1XVlBN8yO7rPhS/common.data"

[[2]]
[1] "/home/xxia/public_html/django/fishcode/static/magicRversion1/data/ZAunc5gFrRetohILTW2/common.data"

[[3]]
[1] "***/SRR12967084.methratio.txt"

[[4]]
[1] "***/SRR12967081.methratio.txt"

[[1]]
[1] "meth_example_01_SRR12967081"

[[2]]
[1] "meth_example_02_SRR12967082"

[[3]]
[1] "SRR12967084"

[[4]]
[1] "SRR12967081"

Received list of locations.
Reading file.
Reading file.
Reading file.
Reading file.
[1] "2023-11-23 12:00:24 CST"
[1] 3
[1] 1000
[1] 1000
[1] 10
uniting...
[1] "methylBase"
attr(,"package")
[1] "methylKit"
'data.frame':	16844 obs. of  16 variables:
Formal class 'methylBase' [package "methylKit"] with 13 slots
  ..@ .Data         :List of 16
  .. ..$ : Factor w/ 1411 levels "NC_002333.2",..: 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ : int  1001 2001 3001 4001 5001 6001 7001 8001 9001 10001 ...
  .. ..$ : int  2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 ...
  .. ..$ : Factor w/ 3 levels "+","-","*": 3 3 3 3 3 3 3 3 3 3 ...
  .. ..$ : num  1607 693 655 1369 2074 ...
  .. ..$ : num  1512 611 596 1221 2023 ...
  .. ..$ : num  95 82 59 148 51 79 160 12 203 49 ...
  .. ..$ : num  843 465 224 674 1318 ...
  .. ..$ : num  816 419 203 637 1309 ...
  .. ..$ : num  27 46 21 37 9 19 105 1 4 3 ...
  .. ..$ : num  1095 389 366 1027 1692 ...
  .. ..$ : num  1072 345 360 986 1651 ...
  .. ..$ : num  23 44 6 41 41 15 22 6 59 11 ...
  .. ..$ : num  1607 693 655 1369 2074 ...
  .. ..$ : num  1512 611 596 1221 2023 ...
  .. ..$ : num  95 82 59 148 51 79 160 12 203 49 ...
  ..@ sample.ids    : chr  "meth_example_01_SRR12967081" "meth_example_02_SRR12967082" "SRR12967084" "SRR12967081"
  ..@ assembly      : chr "own_design"
  ..@ context       : chr "CpG"
  ..@ treatment     : num  0 1 1 0
  ..@ coverage.index: num  5 8 11 14
  ..@ numCs.index   : num  6 9 12 15
  ..@ numTs.index   : num  7 10 13 16
  ..@ destranded    : logi FALSE
  ..@ resolution    : chr "region"
  ..@ names         : chr  "chr" "start" "end" "strand" ...
  ..@ row.names     : int  1 2 3 4 5 6 7 8 9 10 ...
  ..@ .S3Class      : chr "data.frame"
NULL
'data.frame':	3 obs. of  1 variable:
 $ batch_id: chr  "dataset" "PRJNA673886" "PRJNA673886"
NULL
[1] "methylBase"
attr(,"package")
[1] "methylKit"
[1] "*None of the principal components have a relationship with the batch effect that matches your deletion*"
Warning messages:
1: In split.default(x, annot) :
  data length is not a multiple of split variable
2: In split.default(x, annot) :
  data length is not a multiple of split variable
3: In split.default(x, annot) :
  data length is not a multiple of split variable
4: In split.default(x, annot) :
  data length is not a multiple of split variable
5: In split.default(x, annot) :
  data length is not a multiple of split variable
6: In split.default(x, annot) :
  data length is not a multiple of split variable
7: In split.default(x, annot) :
  data length is not a multiple of split variable
8: In split.default(x, annot) :
  data length is not a multiple of split variable
          chr start  end strand coverage1 numCs1 numTs1 coverage2 numCs2 numTs2
1 NC_002333.2  1001 2000      *      1607   1512     95       843    816     27
2 NC_002333.2  2001 3000      *       693    611     82       465    419     46
3 NC_002333.2  3001 4000      *       655    596     59       224    203     21
4 NC_002333.2  4001 5000      *      1369   1221    148       674    637     37
5 NC_002333.2  5001 6000      *      2074   2023     51      1318   1309      9
6 NC_002333.2  6001 7000      *       709    630     79       481    462     19
  coverage3 numCs3 numTs3 coverage4 numCs4 numTs4
1      1095   1072     23      1607   1512     95
2       389    345     44       693    611     82
3       366    360      6       655    596     59
4      1027    986     41      1369   1221    148
5      1692   1651     41      2074   2023     51
6       688    673     15       709    630     79
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
