Description Usage Arguments Value Examples
This function analyses methylome data.
1 2 3 4 5 | analyse_meth(gene, meth_data, meth_platform, probe_idx,
pf_chr_colname = "Chromosome", pf_pos_colname = "Start", PLOT = TRUE,
up_str = 5000, dwn_str = 5000, win_size = 1500, wig_size = 50,
JUST_PROBE_POS = FALSE, GAUSSIAN_MIXTURE = TRUE, mat_mult = function(A,
B) { A %*% B })
|
gene |
A vector describing the gene (line of a bed file). |
meth_data |
A matrix of beta values. |
meth_platform |
A data frame describing CpG positions. |
probe_idx |
A vector specifying probes associated to the gene. |
pf_chr_colname |
string matching the name of the column in the platform that contain the chromosome on which we find a probes. |
pf_pos_colname |
string matching the name of the column in the platform that contain the position information of probes. |
PLOT |
A boolean defining if graphical output must be dispayed on the graphical output. |
up_str |
An integer specifying up stream size (in bp). |
dwn_str |
An integer specifying down stream size (in bp). |
win_size |
An integer specifying slidding window size (in bp). |
wig_size |
An integer specifying wiggle size (in bp). |
JUST_PROBE_POS |
A boolean defining if function returns only probes positions. |
GAUSSIAN_MIXTURE |
A boolean specifying if gaussian mixture model is use to convolve signal. |
mat_mult |
A function to multiply matrices. |
A matrix of convolved probes signal around the TSS of the selected gene.
1 2 3 4 5 6 7 | cols = as.numeric(sunexp_design$sex) * 2
names(cols) = rownames(sunexp_design)
gene = genes[1,]
res1 = analyse_meth(gene, sunexp_data, sunexp_platform)
plot_meth(res1, cols)
legend("topright", col=as.numeric(unique(sunexp_design$sex)) * 2,
legend=unique(sunexp_design$sex), lty=1)
|
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