Description Usage Arguments Value
process_diff_haib_caltech
is a wrapper method ...
1 2 3 4 5 | process_diff_haib_caltech(bs_contr_files, bs_treat_files, rna_contr_files,
rna_treat_files, chrom_size_file = NULL, chr_discarded = NULL,
upstream = -100, downstream = 100, min_bs_cov = 0, max_bs_cov = 1000,
cpg_density = 1, sd_thresh = 0, ignore_strand = FALSE, fmin = -1,
fmax = 1)
|
bs_contr_files |
The name of the control BS-Seq '.bed' formatted files to read data values from. |
bs_treat_files |
The name of the treatment BS-Seq '.bed' formatted files to read data values from. |
rna_contr_files |
The name of the control RNA-Seq '.bed' formatted files to read data values from. |
rna_treat_files |
The name of the treatment RNA-Seq '.bed' formatted files to read data values from. |
chrom_size_file |
Optional name of the file containing genome chromosome sizes |
chr_discarded |
A vector with chromosome names to be discarded. |
upstream |
Integer defining the length of bp upstream of TSS. |
downstream |
Integer defining the length of bp downstream of TSS. |
min_bs_cov |
The minimum number of reads mapping to each CpG site. |
max_bs_cov |
The maximum number of reads mapping to each CpG site. |
cpg_density |
Optional integer defining the minimum number of CpGs that
have to be in a methylated region. Regions with less than |
sd_thresh |
Optional numeric defining the minimum standard deviation of the methylation change in a region. This is used to filter regions with no methylation change. |
ignore_strand |
Logical, whether or not to ignore strand information. |
fmin |
Optional minimum range value for region location scaling. Under this version, this parameter should be left to its default value. |
fmax |
Optional maximum range value for region location scaling. Under this version, this parameter should be left to its default value. |
A diff_processHTS
object which contains among others the
following information:
methyl_region
: A list
containing the methylation regions, where each each entry in the list
consists of an L X 3 dimensional matrix, where:
1st col: Contains the locations of the CpGs relative to TSS, where the range (min, max) of possible values is given, by the inputs fmin and fmax.
2nd col: The total reads of the CpG in the corresponding location.
3rd col: The methylated reads of the CpG in the corresponding location.
prom_region
: A GRanges
object
containing corresponding annotated promoter regions for each entry of the
methyl_region
list..
rna_data
: A GRanges
object
containing the corresponding RNA-Seq data for each entry of the
methyl_region
list.
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