Now that we have a list with all comparisons for replicates (object: "replicates"), pools (object: "pools") and all samples together (allPoolsInOneComparison) we can begin filtering the samples. First idea is to filter by the following params
Usage
analyzer(
SNPcomparison,
minDepthPercentile = 0.1,
maxDepthPercentile = 0.9,
windowSize = 25000,
bulkSize = 20,
outlierFilt = "deltaSNP",
filter_chr_list = NULL
)Arguments
- SNPcomparison
lower tenth percentile > quantile(sum of depth in both bulks, na.rm = T, probs = 0.1))
- minDepthPercentile
sample depth - Half the min depth, Default: 0.9
- maxDepthPercentile
depth: higher fifth percentile > quantile(sum of depth in both bulks, na.rm = T, probs = 0.95)), Default: 0.1
- windowSize
PARAM_DESCRIPTION, Default: 25000
- bulkSize
PARAM_DESCRIPTION, Default: 20
- outlierFilt
see QTLseqR::runGprimeAnalysis, Default: 'deltaSNP'
- filter_chr_list
list of chromosome names to exclude, Default: NULL