Re: [methylkit_discussion] no base were united. try adjusting 'min.per.group'

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Altuna Akalin

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Aug 4, 2020, 7:40:14 AM8/4/20
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please send a reproducible example. It is hard to tell what is going on without such an example in this case.

Best,
Altuna

On Tue, Aug 4, 2020 at 12:29 PM Nilay Can <cann...@gmail.com> wrote:
Hello,

I am trying to unite the filtered samples with this command:

meth_CG2=unite(filtered.myobj_CG2, min.per.group=1L)

where filtered obj is: filtered.myobj_CG2=filterByCoverage(myobj_CpG2,lo.count=5,lo.perc=NULL,
                                hi.count=NULL,hi.perc=99.9)

and

myobj_CpG2=methRead(file.list_CpG2,
               sample.id=list("minus1","minus2","minus3","minus4","plus1","plus2", "plus3"),
               assembly="sim_plant_meth",
               treatment=c(1,1,1,1,0,0,0),
               context="CpG"
)

where the samples have unequal replicates (the first one has four and the second one has three replicates).


and I tried min.per.group=2L and min.per.group=3L too but its keep saying:

Error in unite(filtered.myobj_CG2, min.per.group = 2L)  and Error in unite(filtered.myobj_CG2, min.per.group = 3L) and for 1L too.

What causes this error? Thanks in advance!


Cheers,
Nilay

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Nilay Can

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Aug 4, 2020, 7:51:47 AM8/4/20
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I do not know how you can reproduce the error wo datasets but let me give you more details about my samples. Here is what I got when I call the Obj:

> myobj_CpG2
methylRawList object with 7 methylRaw objects
methylRaw object with 1614314 rows
--------------
         chr start  end strand coverage numCs numTs
1 MA_10g0010  1068 1068      +       21     0    21
2 MA_10g0010  1069 1069      +       10     0    10
3 MA_10g0010  1120 1120      +       34     0    34
4 MA_10g0010  1121 1121      +       14     0    14
5 MA_10g0010  1164 1164      +       28     1    27
6 MA_10g0010  1165 1165      +       12     0    12
--------------
sample.id: minus65 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 345240 rows
--------------
         chr start  end strand coverage numCs numTs
1 MA_10g0010  1068 1068      +       12     0    12
2 MA_10g0010  1120 1120      +       14     0    14
3 MA_10g0010  1164 1164      +       11     0    11
4 MA_10g0010  1171 1171      +       10     0    10
5 MA_10g0010  2247 2247      +       17     0    17
6 MA_10g0010  2283 2283      +       17     0    17
--------------
sample.id: minus67 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 932826 rows
--------------
         chr start  end strand coverage numCs numTs
1 MA_10g0010  1069 1069      +       12     0    12
2 MA_10g0010  1121 1121      +       10     0    10
3 MA_10g0010  1165 1165      +       10     0    10
4 MA_10g0010  1172 1172      +       10     0    10
5 MA_10g0010  2593 2593      +       12     0    12
6 MA_10g0010  2770 2770      +       12     0    12
--------------
sample.id: minus68 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 906616 rows
--------------
         chr start  end strand coverage numCs numTs
1 MA_10g0010  2284 2284      +       14     0    14
2 MA_10g0010  2311 2311      +       10     0    10
3 MA_10g0010  2324 2324      +       10     2     8
4 MA_10g0010  2333 2333      +       10     0    10
5 MA_10g0010  2343 2343      +       10     0    10
6 MA_10g0010  2356 2356      +       10     0    10
--------------
sample.id: minus72 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 997490 rows
--------------
   chr start   end strand coverage numCs numTs
1 MA_2  6095  6095      +       15     2     0
2 MA_2  6119  6119      +       15     2     0
3 MA_2  7068  7068      +       16     3     0
4 MA_2 11812 11812      +       16     2     1
5 MA_2 11824 11824      +       16     0     3
6 MA_2 12842 12842      +       13     2     0
--------------
sample.id: Goeppingen1 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 1004083 rows
--------------
   chr start   end strand coverage numCs numTs
1 MA_2  9526  9526      +       11     1     0
2 MA_2  9556  9556      +       11     1     0
3 MA_2 11812 11812      +       10     0     1
4 MA_2 11813 11813      +       12     1     1
5 MA_2 11824 11824      +       10     0     1
6 MA_2 11825 11825      +       12     0     1
--------------
sample.id: Goeppingen2 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
methylRaw object with 725557 rows
--------------
   chr start   end strand coverage numCs numTs
1 MA_2 11812 11812      +       12     1     1
2 MA_2 11824 11824      +       13     1     1
3 MA_2 12832 12832      +       10     0     1
4 MA_2 12842 12842      +       10     1     0
5 MA_2 12903 12903      +       22     3     2
6 MA_2 12905 12905      +       23     3     3
--------------
sample.id: Goeppingen3 
assembly: sim_plant_meth 
context: CpG 
resolution: base 
treatment: 1 1 1 1 0 0 0 

None of the min.per.group options works. 

I am also pasting the coverage and methylation stats of this Obj. 

coverage.png


methylation.png

Does smt look weird in those graphs to lead this error?

Btw, I also tried another unequal replicates samples and it works well with some..

Here is my whole command up to error point:

file.list_CpG2= list("minus1.txt","minus2.txt","minus3.txt","minus4.txt","plus1.txt","plus2.txt","plus3.txt")

myobj_CpG2=methRead(file.list_CpG2,
               sample.id=list("minus1","minus2","minus3","minus73","plus1.txt","plus2.txt","plus3.txt"),
               assembly="sim_plant_meth",
               treatment=c(1,1,1,1,0,0,0),
               context="CpG"

filtered.myobj_CG2=filterByCoverage(myobj_CpG2,lo.count=5,lo.perc=NULL,
                                hi.count=NULL,hi.perc=99.9)

> meth_CG2=unite(filtered.myobj_CG2, destrand=FALSE)
uniting...
Error in unite(filtered.myobj_CG2, destrand = FALSE) : 
  no base were united. try adjusting 'min.per.group'.
)

I tried using less stringent coverage, also used all min.per.group combinations < 4L but not working..

Thanks!
Best,
Nilay


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Nilay Can

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Aug 4, 2020, 7:57:45 AM8/4/20
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and also please let me know what should I share for you to reproduce the error rather than sharing the datasets.. thanks!


On Tuesday, 4 August 2020 13:40:14 UTC+2, Altuna Akalin wrote:
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Altuna Akalin

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Aug 4, 2020, 8:02:41 AM8/4/20
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chromosome names seem to be different. If they are different unite() won't work. They have to have the same naming convention. 

You can make a reproducible example with subset of the data, that's the main point. Here are some ideas:



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