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
