Obtain_HVP: Obtain High Variable Peak sites

In NWPU-903PR/m6Aexpress: Predicting context-specific m6A regulation of gene expression

Description

This function is to get the high variable peak sites given RNA methylation peak sites under multiple context.

Usage

obtain_HVP_sites(peak_inform,CV_values=0.3,num_sample_subgroup)

Arguments

peak_inform	A list data format, one is dataframe within the consistent peak sites information (e.g. "gene name","seqname","start","end","strand", reads count in each peak of each input samples) under multiple context (e.g. multiple sub-tissues in Brain or Intestine), another is a vector with libray sizes factor to normalize methylation level of each peak site.
CV_values	A decimal number, which is the cutoff for coefficient of variation (CV) used to select high variable peaks. The high variable peaks are defined as CV values are bigger than the cutoff: default CV_values=0.3.
num_sample_subgroup	A vector of integer, which specifies the number of samples for each sub-group. For example, num_sample_subgroup=c(2,2,3,1) means four sub-groups have two samples, two samples, three samples and one sample in each sub-group, respectively.

Details

The high variable peak sites means whose methylation level (log2 ratio for normalized reads count by size factor of each peak site) of each sub-group with higher coefficient of variation value than given cutoff: CV_values across sub-groups.

Value

Results will return a list including the information of high variable peak site in dataframe format and a library size factor in vector format.

high_variable_peak	A dataframe including the information of high variable methylation peak sites
size_factor	A float vector, which specifices the library size factor for IP samples

References

An, Sanqi, et al. "Integrative network analysis identifies cell-specific trans regulators of m6A." Nucleic acids research 48.4 (2020): 1715-1729.

Examples

## Not run: ##Get consist peak site
Get_peak_infor <- Get_peak_sites(IP_BAM, INPUT_BAM,GENE_ANNO_GTF=gtf)
##Detect high variable peak sites
HVP_infor <- obtain_HVP_sites(peak_inform=Get_peak_infor,CV_values=0.3,
                               num_sample_subgroup=c(2,2,2,2))

## End(Not run)

NWPU-903PR/m6Aexpress documentation built on Dec. 17, 2021, 5:18 a.m.