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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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31
unparalogMutations.R
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@ -1,20 +1,30 @@
# Installing missing dependencies
dependencies <- c("stringi", "progress")
missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
if(length(missing_packages)) install.packages(missing_packages)
rm(missing_packages,dependencies)
unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
# #<---------------------------->
# # Please include this section when distributing and/or using this code.
# # Please read and abide by the terms of the included LICENSE
# # 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:
# # In the gene column in your SNV annotation if you see something like:
# # e.g. PRAMEF7;PRAMEF8 OR PRAMEF7,PRAMEF8
# # then your mutations annotations have gene paralogs.
# # This script aims to de-couple those paralogs into individual their rows.
# #
# ------------------------
### Info on what to pass as the function parameters:
# # INFO on what to pass as the function parameters:
# Assign correct paralog_separator found in the gene column of your SNV annotations # e.g. if the Gene column has entries like PRAMEF7;PRAMEF8
# then the paralog_separator is ";"
# or set it to whatever separator is used by your SNV annotation software.
@ -28,14 +38,7 @@
# AnnotationColName = Column name in the SNV annotation table where the Amino acid changes are listed
# <--------------->
# Installing missing dependencies
dependencies <- c("stringi", "progress")
missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
if(length(missing_packages)) install.packages(missing_packages)
rm(missing_packages,dependencies)
unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
# Sanity checks
check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
check_annotation_sep <- !any(stringi::stri_detect_fixed(str = DATA$AAChange.refGene, pattern = annotation_separator))