User: new_user6

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new_user60
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Posts by new_user6

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Comment: C: Using genomic ranges to get counts of non-overlapping (non-redundant) regions
... Sorry about that, I already had a Grangeslist object in my environment, should have mentioned that. ...
written 9 weeks ago by new_user60
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Comment: C: Using genomic ranges to get counts of non-overlapping (non-redundant) regions
... Thanks James. The solution was right there, and I did not notice it. Posting so that someone else might find it useful. An excerpt from the function soGGi:::runConsensusRegions does the job. non_overlapping_region_counts<-function(x){ reduced <- reduce(unlist(myGRangesList)) cons ...
written 9 weeks ago by new_user60
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Comment: C: Using genomic ranges to get counts of non-overlapping (non-redundant) regions
... So, findconsensusRegions requires a named character vector as input whereas I have a list of Granges objects. Should I just convert them into named character vectors and store them as a list? Tried looking for more documentation but could not find any examples in the vignette ...
written 9 weeks ago by new_user60
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Comment: C: Using genomic ranges to get counts of non-overlapping (non-redundant) regions
... Mainly because my input is a list of peaks, am not sure that findconsensusRegions uses a list of peaks, and did not find any examples for the input in the documentation ...
written 9 weeks ago by new_user60
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Using genomic ranges to get counts of non-overlapping (non-redundant) regions
... I have a list of peaks as below, sample shown for 2 samples but have more than that > myPeaks $`HindBrain_1` GRanges object with 6906 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 180772-180997 * ...
genomicranges granges grangeslist R written 9 weeks ago by new_user60 • updated 9 weeks ago by James W. MacDonald51k
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DESeq2 interaction term interpretation
... I am posting an example from elsewhere to see if my understanding of interaction term interpretation is right. dds <- makeExampleDESeqDataSet(n=10000,m=12) dds$condition <- factor( c( rep("Ctrl",6), rep("Trt",6) ) ) dds$genotype <- factor(rep(rep(c("WT","MU") ...
deseq2 written 6 months ago by new_user60 • updated 6 months ago by Michael Love26k
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Comment: C: Inclusion/exclusion of levels of a factor
... When I combine the factors to make interpretations easier, then I have several levels to compare via pairwise comparisons dds$combo [1] D2_WT_mock D2_WT_mock D2_WT_mock D2_KO_mock D2_KO_mock D2_KO_mock D2_WT_inf D2_WT_inf D2_WT_inf D2_KO_inf D2_KO_inf D2_KO_inf D6_WT_mock ...
written 6 months ago by new_user60 • updated 6 months ago by Michael Love26k
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Inclusion/exclusion of levels of a factor
... I have the below data: Samples Genotype treatment Time D2_WT_mock1 WT mock D2 D2_WT_mock2 WT mock D2 D2_WT_mock3 WT mock D2 D2_KO_mock1 KO mock D2 D2_KO_mock2 KO mock D2 D2_KO_mock3 K ...
deseq2 written 6 months ago by new_user60 • updated 6 months ago by Michael Love26k

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