diff --git a/CT_GA_count.R b/CT_GA_count.R index fb8ff55..0347d89 100644 --- a/CT_GA_count.R +++ b/CT_GA_count.R @@ -8,6 +8,7 @@ CT_GA_count <- function(SampleID,Ref_Base,Alt_Base){ # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<----------------------------> diff --git a/IsolateCanonicalVariant.R b/IsolateCanonicalVariant.R index 7c89064..7707216 100644 --- a/IsolateCanonicalVariant.R +++ b/IsolateCanonicalVariant.R @@ -12,6 +12,7 @@ IsolateCanonicalVariant <- function (AAchangeAnnotations){ # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<----------------------------> diff --git a/MutResidueFind.R b/MutResidueFind.R index 401d1f8..60edf29 100644 --- a/MutResidueFind.R +++ b/MutResidueFind.R @@ -12,6 +12,7 @@ MutResidueFind <- function(MutationColumn){ # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<----------------------------> diff --git a/MutSiteFind.R b/MutSiteFind.R index ae69cf2..b95c31b 100644 --- a/MutSiteFind.R +++ b/MutSiteFind.R @@ -12,6 +12,7 @@ MutSiteFind <- function(MutationColumn){ # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<----------------------------> diff --git a/ggplotBreaks.R b/ggplotBreaks.R index 0c28a94..28c69eb 100644 --- a/ggplotBreaks.R +++ b/ggplotBreaks.R @@ -6,6 +6,7 @@ ggplotBreaks <- function(range,tick,skip.steps=0){ # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<----------------------------> diff --git a/roundUp.R b/roundUp.R index 1fcad31..5c8fe6d 100644 --- a/roundUp.R +++ b/roundUp.R @@ -1,28 +1,29 @@ roundUp <- function(x,to=10) { # #<----------------------------> - # # 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 2018, Deepankar Chakroborty, All rights reserved. +# # 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 2018, Deepankar Chakroborty, All rights reserved. - # # Author : Deepankar Chakroborty (https://github.com/dchakro) - # # Report issues: https://github.com/dchakro/shared_Rscripts/issues - # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE +# # 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 - # # Adapted from: https://stackoverflow.com/a/44691056 - - # # PURPOSE: - # # 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. - - # # PARAMETERS - # # x : The integer to be rounded - # # to: nearest place to round to - - # # EXAMPLES - # roundUp(465,20) would give 480 - # roundUp(462,5) would give 465 +# # Adapted from: https://stackoverflow.com/a/44691056 + +# # PURPOSE: +# # 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. + +# # PARAMETERS +# # x : The integer to be rounded +# # to: nearest place to round to + +# # EXAMPLES +# roundUp(465,20) would give 480 +# roundUp(462,5) would give 465 to*(x%/%to + as.logical(x%%to)) } diff --git a/summarySE.R b/summarySE.R index 5b2fda9..47b67b0 100644 --- a/summarySE.R +++ b/summarySE.R @@ -5,30 +5,31 @@ if(length(missing_packages)) install.packages(missing_packages) rm(missing_packages,dependencies) summarySE <- function(data=NULL, measurevar=NULL, statistic="mean", groupvars=NULL, na.rm=FALSE, conf.interval=.95, .drop=TRUE) { - # #<----------------------------> - # # 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 2018, Deepankar Chakroborty, All rights reserved. +# #<----------------------------> +# # 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 2018, Deepankar Chakroborty, All rights reserved. - # # Author : Deepankar Chakroborty (https://github.com/dchakro) - # # Report issues: https://github.com/dchakro/shared_Rscripts/issues - # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE +# # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com +# # 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/ - - # # PURPOSE: - # # Summarizes data by returning count, mean, standard deviation, - # # standard error of the mean, and confidence interval (default 95%) - # # for a given data frame based on grouping variables - # # data: a data frame. - - # # PARAMETERS - # # measurevar: the name of a column that contains the variable to be summariezed - # # groupvars: a vector containing names of columns that contain grouping variables - # # na.rm: a boolean that indicates whether to ignore NA's - # # conf.interval: the percent range of the confidence interval (default is 95%) - # #<----------------------------> +# # Adapted from: http://www.cookbook-r.com/Manipulating_data/Summarizing_data/ + +# # PURPOSE: +# # Summarizes data by returning count, mean, standard deviation, +# # standard error of the mean, and confidence interval (default 95%) +# # for a given data frame based on grouping variables +# # data: a data frame. + +# # PARAMETERS +# # measurevar: the name of a column that contains the variable to be summariezed +# # groupvars: a vector containing names of columns that contain grouping variables +# # na.rm: a boolean that indicates whether to ignore NA's +# # 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 length2 <- function (x, na.rm=FALSE) { diff --git a/unparalogMutations.R b/unparalogMutations.R index 1e1698a..f7b1c11 100644 --- a/unparalogMutations.R +++ b/unparalogMutations.R @@ -12,6 +12,7 @@ unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", # # Copyright 2020, Deepankar Chakroborty, All rights reserved. # # # # Author : Deepankar Chakroborty (https://github.com/dchakro) +# # Website: https://www.dchakro.com # # Report issues: https://github.com/dchakro/shared_Rscripts/issues # # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE # #<---------------------------->