User: mrk.carty

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mrk.carty30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
4 years, 1 month ago
Joined:
4 years, 9 months ago
Email:
m********@gmail.com

Posts by mrk.carty

<prev • 7 results • page 1 of 1 • next >
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The distribution function for zero-altered negative binomial density produces a probability greater 1
... Hi all,         I'm using the pzanegbin distribution function from the VGAM package to compute p-value for events coming from hurdle negative binomial regression null distribution. Here are details of the computation: > library(VGAM) Loading required package: stats4 Loading required package ...
vgam pzanegbin written 4.1 years ago by mrk.carty30 • updated 4.1 years ago by Ryan C. Thompson7.4k
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How to read in bam file that is output from presplit_map.py using the GenomicAlignment package
...   Hi all, I've been using the diffHiC package for awhile. I would like to read in the bam file, which is the output after running presplit_map.py, using Rsamtools or GenomicAlignment package. I cannot read in the bam file using either of these packages. However, I can read in the bam file using pr ...
diffhic written 4.4 years ago by mrk.carty30 • updated 4.4 years ago by Aaron Lun25k
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Memory management in R
... Hi everyone, I've written a script to compute p-values based on model estimates from a hurdle regression using pscl package. I'm using the predict() function from the stats package to get estimated mean and zero probabilities need to calculate the p-values. the features are stored in big.memory mat ...
stats written 4.7 years ago by mrk.carty30 • updated 4.7 years ago by Martin Morgan ♦♦ 24k
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Modeling count data that is zero inflated with negative binomial hurdle regression
... Hi all, I am modeling count data that is zero-inflated. To model the data, I am using hurdle() function from the R pscl package. I am also refitting the model after the removal of outlier points. I have written a function to remove outliers from the data set. However, I think there is a bug in the ...
outliers pscl written 4.7 years ago by mrk.carty30 • updated 4.7 years ago by Sean Davis21k
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Performing findOverlaps when both subject and query are on the order of a million
... Hi everyone, I want to do a findOverlaps when both subject and query are very large. My query is a GRanges object of genomic intervals on a particular chromosome (~8 million ranges), and my subject is another GRanges object of roughly 2 million reads. I thought of dividing the queries into smaller ...
findoverlaps written 4.8 years ago by mrk.carty30 • updated 4.8 years ago by Hervé Pagès ♦♦ 14k
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Answer: A: Creating all possible k combinations of n objects with a constraint for large n
... Hi Sean, Thanks a lot! This solution has speed up pipeline. Best, Mark ...
written 4.8 years ago by mrk.carty30
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Creating all possible k combinations of n objects with a constraint for large n
... Hi all, If I have an ordered vector of genomic positions on chr1 > head(positions) [1] 11161 12412 12462 12687 12830 13316 > length(positions) [1] 576356 The distances between consecutive positions is represented by > d <- positions[-1] - positions[-length(positions)] > head(d) ...
base written 4.8 years ago by mrk.carty30

Latest awards to mrk.carty

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Modeling count data that is zero inflated with negative binomial hurdle regression
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Memory management in R

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