Code

Splat pop#106

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lazappi merged 93 commits intoOshlack:masterOshlack/splatter:masterfrom azodichr:splatPopCopy head branch name to clipboardOct 22, 2020

+2,824-33

Commits

Commits on Sep 23, 2020

• first splat-eqtl commit

  

  cazodi

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  lazappi

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  18d7dc9

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• working version of splateQTL

  

  cazodi

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  lazappi

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  04aca4e

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• added eQTL functions to manual section

  

  cazodi

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  lazappi

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  62ed579

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• fixed nGroups not found bug

  

  cazodi

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  lazappi

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  6c9d090

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• update to use vcf and gff object instead of path

  

  cazodi

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  lazappi

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• added vcf and gff example data

  

  cazodi

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  16b0502

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• add eQTL parameters S4 object information

  

  cazodi

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  lazappi

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  1e4ff94

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• add eQTL parameters S4 object information

  

  cazodi

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  2fbb372

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• added eQTLEstimate function and eqtl params as an S4 parameters object

  

  cazodi

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  c3900c9

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• fixing r check errors

  

  cazodi

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  eee64ed

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• fix r check bug

  

  cazodi

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• remove example datafiles from git

  

  cazodi

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• testing

  

  Christina Azodi

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  9bb0daf

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• fix bug with infinit gene means

  

  cazodi

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  24a8ca8

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• fixed error with mean being assigned as Inf if pnorm was = 0

  

  cazodi

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• bug fix colnames to names

  

  cazodi

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  cd7ac9e

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• added testthat tests for eQTL functions

  

  cazodi

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• added random seed

  

  cazodi

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• added eQTL to vignette

  

  cazodi

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  a4b6db8

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• minor bug

  

  cazodi

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  990e448

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• update eqtlSimulate to simulate groups

  

  cazodi

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  lazappi

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  07b3ec2

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• added group-specific eqtl params to eqtl-params

  

  cazodi

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  lazappi

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  66c8f93

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• adding group specific eQTL

  

  cazodi

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  6f0f50c

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• fixed r check bugs since group-specific eQTL added

  

  cazodi

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  a767cf3

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• major speed improvement

  

  cazodi

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  1bb7db9

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• first wave of faster code for eQTL-splatter

  

  cazodi

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  999e982

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• fix bug with only g1 specific eqtl having effect

  

  cazodi

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  2d1abb0

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• second try at fixing only getting g1 specific eqtl bug

  

  cazodi

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  81bf58e

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• adds eQTL effects to un-normalized gene means

  

  cazodi

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  lazappi

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• apply eQTL effects on rnorm means using true, not normalized, means

  

  cazodi

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  lazappi

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  c17bd4e

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• add non-eqtl group effects and update quantile normalization function to allow for user provided bulk data

  

  cazodi

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  lazappi

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• remove header requirements for input vcf

  

  cazodi

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  56a4c3d

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• keep gene start and stop in key

  

  cazodi

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  257e842

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• updates based on jeffreys comments. Round 1

  

  cazodi

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  d0a2713

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• updates from r check

  

  cazodi

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  lazappi

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  db10f8c

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• update from eqtl to pop

  

  cazodi

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  lazappi

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  551437b

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• Tweak R code and formatting

  

  jeffreypullin

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  lazappi

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  a390d91

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• updated naming from eqtl to pop, added functions to randomly genenrate genes, removed depencies on package data

  

  cazodi

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  f5cc8c4

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• Tidy files

  lazappi

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Commits on Oct 2, 2020

• add splatParams objects to splatPopParams

  

  cazodi

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Commits on Oct 7, 2020

• update tests

  

  cazodi

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  20ca3c0

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• moved splatPop functions out of base splat scripts

  

  cazodi

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• fixed but in updated splatPopParam

  

  cazodi

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• moved splatPop to separate vignette

  

  cazodi

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  f127c65

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• minor bug fix

  

  cazodi

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• minor bug fixes

  

  cazodi

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  0f0084c

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• Update splat-estimate.R

  azodichr

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• update vignette to remove devtools

  

  cazodi

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• removed commenting out of clean up step

  

  cazodi

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• Merge branch 'splatPop' of https://github.com/azodichr/splatter into splatPop

  

  cazodi

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• removed commenting out of clean up step

  

  cazodi

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• Tidy whitespace

  lazappi

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• Tidy whitespace in test-splat-simulate.R

  lazappi

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Commits on Oct 8, 2020

• fix small bug with vcfR input with ID

  

  cazodi

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  902df0f

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• fix minor bug with nGenes param not updating

  

  cazodi

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  c4cc285

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• Merge branch 'splatPop' of https://github.com/azodichr/splatter into splatPop

  

  cazodi

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Commits on Oct 10, 2020

• added MAF to splatPop key

  

  cazodi

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• removed random.genes from splatPopParams. Replace with logical method for gene selection key > gff > random

  

  cazodi

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• minor update to eqtl eq

  

  cazodi

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Commits on Oct 13, 2020

• Update R/mock-data.R

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  azodichr

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  lazappi

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• updates following code review by Luke

  

  cazodi

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• merge mock-data

  

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Commits on Oct 15, 2020

• merge outputs into sce object

  

  cazodi

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Commits on Oct 18, 2020

• switched from vcfR to VariantAnnotate

  

  cazodi

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• update vignette

  

  cazodi

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Commits on Oct 19, 2020

• Pass params to splatEstimate() in splatPopeEstimate()

  lazappi

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• Adjust vignette chunk options

  lazappi

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• Fix namespace warnings

  lazappi

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  cf0ab96

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• Tidy up suggested package checks

  lazappi

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  d1a8da5

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• updates to vignette

  

  cazodi

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Commits on Oct 21, 2020

• updates to vignette and only check assertClass in newSplatPopParams

  

  cazodi

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• removed unneeded exports

  

  cazodi

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• add eSNP chromo and loc to output sce

  

  cazodi

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• Replace 1:x with seq_len()

  lazappi

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  1c01f3a

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• Adjust number of columns in splatPopSimulate key test

  lazappi

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  96d6c64

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• Fix missing package references

  lazappi

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  74c1de8

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• Remove references to splatPopParams in splatEstimate

  lazappi

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• Remove default in splatSimulate docs

  lazappi

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• Rename splatPopParams to SplatPopParams

  lazappi

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• Remove unnecessary namespace checks

  lazappi

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• Rename Data.frame to data.frame in function docs

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• Remove unrelated paragraph from splatPopEstimateMeanCV docs

  lazappi

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• Move checks to start of newSplatPopParams()

  lazappi

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• Delete commented line in SplatPopParms show method

  lazappi

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• Remove SplatParams check in SplatPopParams setParams method

  lazappi

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• Remove global variables

  lazappi

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• Remove SplatParams tests from test-SplatPopParams

  lazappi

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• Use matrix for population means

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• Add package checks to splatPop tests

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• Proofread splatPop vignette

  lazappi

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Commits on Oct 22, 2020

• add christina as contributor

  

  cazodi

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• Bump version number and update NEWS

  lazappi

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• Minor Splatter vignette fixes

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