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Add CT_GA_count.R

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commit ec4f4915ebf6dfda264a5b58c0e180a47e948b99
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Fri Jul 31 13:23:36 2020 +0300

    Removed testing code

commit c1fddc713c1d18bd4272b2c455425931681dafe1
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Fri Jul 31 13:23:14 2020 +0300

    Fixed subsetting to make it work

commit a64df5c0d15cce8ce2ad78a019cafc9aa17b5ff0
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Fri Jul 31 13:16:28 2020 +0300

    add CT_GA_count.R

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 13:24:28 +03:00
parent 52554283f1
commit d4465971e0
1 changed files with 62 additions and 0 deletions
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CT_GA_count.R Normal file
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CT_GA_count <- function(SampleID,Ref_Base,Alt_Base){
# #<---------------------------->
# # 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:
# # This function takes in three vectors:
# # SampleID = Sample IDs
# # Ref_Base = Reference Base
# # Alt_Base = altered base that created the mutation.
# # And calculates the number of C > T and G > A changes are there (per sample)
# # The function returns a data frame listing the number of mutations (per sample):
# # SampleID = Sample ID
# # Total = Total number of mutations
# # CT = C > T changes
# # GA = G > A changes
# # Others = all other types of transitions and transversions combined.
MutMatrix <- data.frame(SampleID,
Ref_Base,
Alt_Base,
stringsAsFactors = F)
return.df <- data.frame(SampleID=NA,
Total=0,
CT=0,
GA=0,
Others=0)
for(SampleID in levels(MutMatrix$SampleID)){
set <- MutMatrix[ MutMatrix$SampleID == SampleID, ]
# if(dim(set)[1]==0){
# return.df <- rbind.data.frame(return.df,c(SampleID,0,0,0,0))
# next
# }
Total <- dim(set)[1]
CT <- dim(subset(set, set$Ref_Base == "C" & set$Alt_Base == "T"))[1]
GA <- dim(subset(set, set$Ref_Base == "G" & set$Alt_Base == "A"))[1]
Others=Total-CT-GA
return.df <- rbind.data.frame(return.df,list(SampleID,Total,CT,GA,Others),stringsAsFactors = F)
Total <- 0;CT <- 0;GA <- 0;Others <- 0 # re-initialize
rm(set)
}
return(return.df[-1,]) # Removes the first empty row
}