addPatternDensity to qsea object
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Entering edit mode
12 weeks ago
Jaykishan • 0

i have qsea object contain 6 sample with 11 chromosome where i am trying to addPatternDensity which is by default 0.01

qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.1)

when i am trying to change it like this with following values it through me error

qseaSet <- addPatternDensity(qseaSet, pattern = "CG", name = "CpG", maxPatternDensity = 0.1) Error in addPatternDensity(qseaSet, pattern = "CG", name = "CpG", maxPatternDensity = 0.1) : unused argument (maxPatternDensity = 0.1)

qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.05) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 0.05 per fragment found to estimate background read distribution qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.1) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 0.1 per fragment found to estimate background read distribution qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.5) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 0.5 per fragment found to estimate background read distribution qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.8) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 0.8 per fragment found to estimate background read distribution qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 0.10) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 0.1 per fragment found to estimate background read distribution qseaSet <- addOffset(qseaSet, enrichmentPattern = "CpG", maxPatternDensity = 1.0) selecting windows with low CpG density for background read estimation Error in estimateOffset(qs, enrichmentPattern, maxPatternDensity) : not enough windows with enrichment pattern density of at most 1 per fragment found to estimate background read distribution

please guide me through possible solution

maxDensityPattern medip qsea • 157 views
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