add_2OmeScore | R Documentation |
Methylation score that considers the log2-FCH of start ratio between two RNA-seq libraries (low-dNTPs and high-dNTPs), subtracting the "noise" from a surrounding window.
add_2OmeScore( STORM, lib_LowdNTPs, lib_HighdNTPs, newColName = "auto", flankSize = 5, perNuc_Zscaling = F, onNucs = c("A", "C", "G", "T"), minCov = 50 )
STORM |
list. STORM object as output by |
lib_LowdNTPs |
character. Name of group with low-dNTPs library preparation found in STORM$META$group |
lib_HighdNTPs |
character. Name of group with high-dNTPs library preparation found in STORM$META$group |
newColName |
character. Name of calculated metric to be stored in STORM$RES, assigned by default based on group_A and group_B |
flankSize |
integer. Length of window to each side of position to consider for metric calculation |
onNucs |
character. Nucleotide(s) in which the metric will be calculated |
minCov |
integer. Minimal coverage in position for metric to be calculated |
Incarnato et al. 2017: For Nm Incarnato and collabs. used the fold change as the log2 of the ratio between the stoppage ratio at the low dNTPs concentration and the stoppage ratio in the high dNTPs concentration sample. Because the stoppage ratio seems to be strongly region specific, they subtracted the local background defined as the mean ratio of the stoppage in the neighborhood of a given position (+/- 5 nucleotides, excluding given position).
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