mirror of
https://github.com/dchakro/shared_Rscripts.git
synced 2026-05-18 09:14:44 -07:00
d4465971e0
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
62 lines
2.1 KiB
R
62 lines
2.1 KiB
R
|
|
|
|
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
|
|
}
|