ChIP-seq peak notes

[mariam16548]

My notes for the first paper:

• Peak calling with ChIP-seq data comes with an issue of identifying candidate peaks (which ones denote a tf binding sites vs. those that are "experimental noise", or something else)
• In order to combat this problem, they surveyed 30 different methods to see which was best.
• They found that peak detection was reduced when ChIP and input signals are explicitly combined. (Even after doing extra research on it, I'm still not sure what this exactly means)
• For statistical significance, they found methods using a Poisson test to rank the peaks, is more powerful than the Binomial test.
• Also, using windows of different sizes to scan the genome for potential peaks is more powerful than not using different sizes.

Notes for the more recent paper (Grytten):

• The developed a tool called "Graph Peak Caller" based on MACS2
• They used A. thaliana to conduct the study, showing that the peaks found by Graph Peak Caller, in general, are "more enriched for DNA-binding motifs than those found by MACS2 on a linear reference genome".

Here is the source for the paper I was looking over (published in May 2016, appeared in the journal in May 2017): https://doi.org/10.1093/bib/bbw035 Reuben Thomas, Sean Thomas, Alisha K Holloway, Katherine S Pollard, Features that define the best ChIP-seq peak calling algorithms, Briefings in Bioinformatics, Volume 18, Issue 3, May 2017, Pages 441–450, https://doi.org/10.1093/bib/bbw035

The other one I spoke to you about (published in February of 2019): https://doi.org/10.1371/journal.pcbi.1006731 Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019) Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput Biol 15(2): e1006731. https://doi.org/10.1371/journal.pcbi.1006731

[paul-shannon]

Very helpful, Mariam - thanks!

With this information archived on github, please set this question aside until I hear back from our colleagues.

Please move on to understand

• default function arguments (aka, default parameters)
• using the function is.na(arg) to test for their presence

• write some exploratory code, a function that does something trivial (like uppercase a string) using a default argument. you can call the function in two ways: using the default, overriding the default

  uppercaseString <- function(targetString=NA)){ if(is.na(targetString)) return(“THIS IS A DEFAULT STRING”) return(topper(targetString)

Not a very useful function. But it demonstrates the use of defaults and testing for NA

On Jul 23, 2019, at 1:35 PM, mariam16548 notifications@github.com wrote:

My notes for the first paper:

• Peak calling with ChIP-seq data comes with an issue of identifying candidate peaks (which ones denote a tf binding sites vs. those that are "experimental noise", or something else) • In order to combat this problem, they surveyed 30 different methods to see which was best. • They found that peak detection was reduced when ChIP and input signals are explicitly combined. (Even after doing extra research on it, I'm still not sure what this exactly means) • For statistical significance, they found methods using a Poisson test to rank the peaks, is more powerful than the Binomial test. • Also, using windows of different sizes to scan the genome for potential peaks is more powerful than not using different sizes. Notes for the more recent paper (Grytten):

• The developed a tool called "Graph Peak Caller" based on MACS2 • They used A. thaliana to conduct the study, showing that the peaks found by Graph Peak Caller, in general, are "more enriched for DNA-binding motifs than those found by MACS2 on a linear reference genome". Here is the source for the paper I was looking over (published in May 2016, appeared in the journal in May 2017): https://doi.org/10.1093/bib/bbw035 Reuben Thomas, Sean Thomas, Alisha K Holloway, Katherine S Pollard, Features that define the best ChIP-seq peak calling algorithms, Briefings in Bioinformatics, Volume 18, Issue 3, May 2017, Pages 441–450, https://doi.org/10.1093/bib/bbw035

The other one I spoke to you about (published in February of 2019): https://doi.org/10.1371/journal.pcbi.1006731 Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019) Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput Biol 15(2): e1006731. https://doi.org/10.1371/journal.pcbi.1006731

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