demuellae
commented
4 years ago Unfortunately. Non-CpG methylation analysis is currently not supported by RnBeads. This is a feature that we planned for, but have not yet fully implemented. If you really wanted to analyze nonCGs, you would have to create a new annotation package.
Hello, I am facing problems in using RnBeads to identify differentially methylated Cytosins in "CH" context. The methylation calls are from biseqMethCalling. I could analyze "CG" context data successfully. But the package doesn't work for "CHH" context. I am getting the following error.
2019-10-01 19:34:21 1.5 STATUS STARTED RnBeads Pipeline 2019-10-01 19:34:21 1.5 INFO Initialized report index and saved to index.html 2019-10-01 19:34:21 1.5 STATUS STARTED Loading Data 2019-10-01 19:34:21 1.5 INFO Number of cores: 1 2019-10-01 19:34:22 1.5 INFO Loading data of type "bs.bed.dir" 2019-10-01 19:34:22 1.5 STATUS STARTED Performing loading test 2019-10-01 19:34:22 1.5 INFO The first 10000 rows will be read from ea ch data file 2019-10-01 19:34:22 1.5 INFO No column with file names specified: will try to find one 2019-10-01 19:34:22 1.5 STATUS STARTED Loading Data From BED Files 2019-10-01 19:34:23 1.6 STATUS STARTED Automatically parsing the pro vided sample annotation file 2019-10-01 19:34:23 1.6 STATUS Potential file names found in col umn 1 of the supplied annotation table 2019-10-01 19:34:23 1.6 STATUS COMPLETED Automatically parsing the p rovided sample annotation file 2019-10-01 19:34:23 1.6 INFO Reading BED file: /sfs/lustre/bahamut /scratch/mcm3ha/RRBS/beds/RRBS_cphphMethylation_Cre1.bed 2019-10-01 19:34:24 1.6 INFO Reading BED file: /sfs/lustre/bahamut /scratch/mcm3ha/RRBS/beds/RRBS_cphphMethylation_Cre2.bed 2019-10-01 19:34:25 1.6 STATUS Read 2 BED files 2019-10-01 19:34:25 1.6 STATUS Matched chromosomes and strands to an notation 2019-10-01 19:34:25 1.6 STATUS Checked for the presence of sites and coverage 2019-10-01 19:34:25 1.6 STATUS Initialized meth/covg matrices opening ff /sfs/lustre/bahamut/scratch/mcm3ha/tmp/RtmpR5YiyV/ff265f7576e135d.ff 2019-10-01 19:34:25 1.6 STATUS Combined a data matrix with 13153 sit es and 2 samples 2019-10-01 19:34:25 1.6 STATUS Processed all BED files 2019-10-01 19:34:25 1.6 STATUS STARTED Creating RnBiseqSet object 2019-10-01 19:34:55 4.2 WARNING All sites have been removed, returning NULL 2019-10-01 19:34:55 4.2 STATUS COMPLETED Creating RnBiseqSet object 2019-10-01 19:34:55 4.2 STATUS COMPLETED Loading Data From BED Files 2019-10-01 19:34:55 4.2 STATUS STARTED Checking the loaded object 2019-10-01 19:34:55 4.2 INFO The supplied object is not of class RnBiseqSet. Breaking the check... 2019-10-01 19:34:55 4.2 WARNING The object loaded during the loading test contains invalid information (see details above). Please check the whether the data source arguments as well as the data import options, like table separator, BED style or BED column assignment, are set correctly
I found the following difference between bed files of CG and CHH context. In CG context bed file, the value on the 5th column = fraction from 4th column * 1000 This is not true with the CpHpH context bed file. Will this make any problem in running the package?
below are the snapshots of the bed files
CG context bed file chr1 3014927 3014929 '0/1' 0 - chr1 3014973 3014975 '2/2' 1000 - chr1 3015684 3015686 '54/54' 1000 - chr1 3016214 3016216 '4/4' 1000 + chr1 3016283 3016285 '34/40' 850 + chr1 3016620 3016622 '28/29' 966 - chr1 3020876 3020878 '1/1' 1000 - chr1 3020890 3020892 '26/26' 1000 - chr1 3020944 3020946 '26/26' 1000 - chr1 3027016 3027018 '32/32' 1000 -
CpHpH context chr1 3042577 3042580 '0/21' 0 + chr1 3042586 3042589 '0/21' 0 + chr1 3042588 3042591 '0/21' 0 + chr1 3042589 3042592 '1/21' 500 + chr1 3042600 3042603 '0/21' 0 + chr1 3042605 3042608 '0/21' 0 + chr1 3042612 3042615 '3/21' 571 + chr1 3042618 3042621 '1/21' 500 + chr1 3043054 3043057 '0/10' 0 + chr1 3043058 3043061 '0/10' 0 + chr1 3043063 3043066 '0/10' 0 + chr1 3043064 3043067 '0/10' 0 +