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dchakro 2020-12-16 19:38:29 +02:00
parent db75cd3575
commit 03836a5c29
8 changed files with 50 additions and 42 deletions
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1
CT_GA_count.R
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@ -8,6 +8,7 @@ CT_GA_count <- function(SampleID,Ref_Base,Alt_Base){
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->

1
IsolateCanonicalVariant.R
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@ -12,6 +12,7 @@ IsolateCanonicalVariant <- function (AAchangeAnnotations){
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->

1
MutResidueFind.R
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@ -12,6 +12,7 @@ MutResidueFind <- function(MutationColumn){
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->

1
MutSiteFind.R
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@ -12,6 +12,7 @@ MutSiteFind <- function(MutationColumn){
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->

1
ggplotBreaks.R
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@ -6,6 +6,7 @@ ggplotBreaks <- function(range,tick,skip.steps=0){
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->

35
roundUp.R
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@ -1,28 +1,29 @@
roundUp <- function(x,to=10) roundUp <- function(x,to=10)
{ {
# #<----------------------------> # #<---------------------------->
# # You must include this section when: # # You must include this section when:
# # Distributing, Using and/or Modifying this code. # # Distributing, Using and/or Modifying this code.
# # Please read and abide by the terms of the included LICENSE. # # Please read and abide by the terms of the included LICENSE.
# # Copyright 2018, Deepankar Chakroborty, All rights reserved. # # Copyright 2018, Deepankar Chakroborty, All rights reserved.
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # Website: https://www.dchakro.com
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# # Adapted from: https://stackoverflow.com/a/44691056 # # Adapted from: https://stackoverflow.com/a/44691056
# # PURPOSE: # # PURPOSE:
# # This function takes in single number as input and rounds it # # This function takes in single number as input and rounds it
# # to the nearest tenth by default. e.g. 7 would be rounded to 10. # # to the nearest tenth by default. e.g. 7 would be rounded to 10.
# # PARAMETERS # # PARAMETERS
# # x : The integer to be rounded # # x : The integer to be rounded
# # to: nearest place to round to # # to: nearest place to round to
# # EXAMPLES # # EXAMPLES
# roundUp(465,20) would give 480 # roundUp(465,20) would give 480
# roundUp(462,5) would give 465 # roundUp(462,5) would give 465
to*(x%/%to + as.logical(x%%to)) to*(x%/%to + as.logical(x%%to))
} }

41
summarySE.R
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@ -5,30 +5,31 @@ if(length(missing_packages)) install.packages(missing_packages)
rm(missing_packages,dependencies) rm(missing_packages,dependencies)
summarySE <- function(data=NULL, measurevar=NULL, statistic="mean", groupvars=NULL, na.rm=FALSE, conf.interval=.95, .drop=TRUE) { summarySE <- function(data=NULL, measurevar=NULL, statistic="mean", groupvars=NULL, na.rm=FALSE, conf.interval=.95, .drop=TRUE) {
# #<----------------------------> # #<---------------------------->
# # You must include this section when: # # You must include this section when:
# # Distributing, Using and/or Modifying this code. # # Distributing, Using and/or Modifying this code.
# # Please read and abide by the terms of the included LICENSE. # # Please read and abide by the terms of the included LICENSE.
# # Copyright 2018, Deepankar Chakroborty, All rights reserved. # # Copyright 2018, Deepankar Chakroborty, All rights reserved.
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Website: https://www.dchakro.com
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# # Adapted from: http://www.cookbook-r.com/Manipulating_data/Summarizing_data/ # # Adapted from: http://www.cookbook-r.com/Manipulating_data/Summarizing_data/
# # PURPOSE: # # PURPOSE:
# # Summarizes data by returning count, mean, standard deviation, # # Summarizes data by returning count, mean, standard deviation,
# # standard error of the mean, and confidence interval (default 95%) # # standard error of the mean, and confidence interval (default 95%)
# # for a given data frame based on grouping variables # # for a given data frame based on grouping variables
# # data: a data frame. # # data: a data frame.
# # PARAMETERS # # PARAMETERS
# # measurevar: the name of a column that contains the variable to be summariezed # # measurevar: the name of a column that contains the variable to be summariezed
# # groupvars: a vector containing names of columns that contain grouping variables # # groupvars: a vector containing names of columns that contain grouping variables
# # na.rm: a boolean that indicates whether to ignore NA's # # na.rm: a boolean that indicates whether to ignore NA's
# # conf.interval: the percent range of the confidence interval (default is 95%) # # conf.interval: the percent range of the confidence interval (default is 95%)
# #<----------------------------> # #<---------------------------->
# a version of length which can handle NA's: if na.rm==T, don't count them # a version of length which can handle NA's: if na.rm==T, don't count them
length2 <- function (x, na.rm=FALSE) { length2 <- function (x, na.rm=FALSE) {

1
unparalogMutations.R
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@ -12,6 +12,7 @@ unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",",
# # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # Copyright 2020, Deepankar Chakroborty, All rights reserved.
# # # #
# # Author : Deepankar Chakroborty (https://github.com/dchakro) # # Author : Deepankar Chakroborty (https://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<----------------------------> # #<---------------------------->