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rargelaguet / scnmt_gastrulation

scNMT-seq gastrulation
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questions about variable names #3

Closed yuhanH closed 3 years ago

yuhanH commented 3 years ago

HI, Ricard @rargelaguet I am wondering what variables in the Methylation data represent. Rate seems to represent the beta value for the aggregated regions. What the meaning of Nmet and N? Can I use N and Nmet to obtain rate?

             id_met                 id           anno Nmet N rate
1: E7.5_Plate12_H02 ENSMUSG00000000001 prom_2000_2000    0 4    0
2: E7.5_Plate12_H02 ENSMUSG00000000049 prom_2000_2000    0 5    0
3: E7.5_Plate12_H02 ENSMUSG00000000085 prom_2000_2000    0 3    0
4: E7.5_Plate12_H02 ENSMUSG00000000120 prom_2000_2000    1 7   14
5: E7.5_Plate12_H02 ENSMUSG00000000126 prom_2000_2000    0 5    0
6: E7.5_Plate12_H02 ENSMUSG00000000148 prom_2000_2000    0 7    0

Thanks for your help!

rargelaguet commented 3 years ago

Hi Yuhan, Nmet is the number of methylated CpGs within that cell and genomic region, and N is the total number of CpGs. Then, rate = 100*Nmet/N.

FYI These files are created with the following script: https://github.com/rargelaguet/scnmt_gastrulation/blob/master/metacc/annotate/annotate.R

yuhanH commented 3 years ago

Thanks for your rapid reply!