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commit fe050d47c2dc9e61a13d4a362abf56dabfbecbd7
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Fri Jul 31 12:57:11 2020 +0300

    Include usage instruction inside function body

    Include usage instruction inside function body, so on typing just the function name to display the R code, the instructions will appear.
    Also stated things clearly in the T&C

commit fedbca4a7aa8fb436702accdf1f9b5ec7f066d60
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:50:20 2020 +0300

    Updates

    1. Improve readability
    2. Manage differing lengths of breaks and labels.

commit fb32fb9173c66c8862adb0ad41d82db9d128777b
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:43:20 2020 +0300

    skip.steps works as expected

    skip.steps = 1, now skips 1 observation.

commit 00a8bbcf04731c010e0a5989a805274609560188
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Thu Jul 30 12:32:16 2020 +0300

    add script to calculate breaks for axes in ggplot2

    calculates breaks and labels for axes in ggplot2 with user defined gaps
This commit is contained in:
Deepankar Chakroborty 2020-07-31 12:58:00 +03:00
parent f9f647c131
commit 52554283f1
4 changed files with 72 additions and 61 deletions
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48
IsolateCanonicalVariant.R
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@ -1,26 +1,3 @@
# #<---------------------------->
# # Please include this section when distributing and/or using this code.
# # Please read and abide by the terms of the included LICENSE
# #
# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
# #
# # PURPOSE:
# # From a given vector of annotations for a particular DNA change
# # this function selects the canonical variant (if present)
# # by cross referencing the MANE Select and RefSeq Select sets.
# #
# # Logic flow:
# # - If there is only one annotation; that is selected
# # - If canonical transcript is not found in MANE Select + RefSeq select
# # or a matching transcript ID is not found in the annotation then;
# # The mutation with to the the highest position (residue number) is selected.
# # - If a match for canonical isoform is found then;
# # that particular mutation is selected
# #
# #<---------------------------->
# Installing dependencies
dependencies <- c("stringi", "doParallel")
missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
@ -28,6 +5,31 @@ if(length(missing_packages)) install.packages(missing_packages)
rm(missing_packages,dependencies)
IsolateCanonicalVariant <- function (AAchangeAnnotations){
# #<---------------------------->
# # You must include this section when:
# # Distributing, Using and/or Modifying this code.
# # Please read and abide by the terms of the included LICENSE.
# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# #
# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
# #<---------------------------->
# # PURPOSE:
# # From a given vector of annotations for a particular DNA change
# # this function selects the canonical variant (if present)
# # by cross referencing the MANE Select and RefSeq Select sets.
# # LOGIC FLOW:
# # - If there is only one annotation; that is selected
# # - If canonical transcript is not found in MANE Select + RefSeq select
# # or a matching transcript ID is not found in the annotation then;
# # The mutation with to the the highest position (residue number) is selected.
# # - If a match for canonical isoform is found then;
# # that particular mutation is selected
# importing resources
library(doParallel)
refseq <- readRDS(url("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/master/asset/RefSeqSelect_Gene_Transcript.RDS"),"rb")