| #' @function survival analysis according to gene expression for primary tumor | |
| #' @param geneSymbol identify gene symbol | |
| #' @param exp TCGA format gene expression dataset | |
| #' @param cli Clinical information dataset | |
| #' @param method method use to dive samples into groups. Options are "quantile", "median", "mean". the "quartile" use first and third quartile as threshold | |
| #' @param trans transform the clinical IDs from '-' separate to '.' separate | |
| #' @return include the plot and p value | |
| #' @author Shixiang Wang | |
| # input test data |
| T_test = function(data, group1, group2, adj.method="fdr"){ | |
| # the first column of data is identifier | |
| # the others columns cotain gene expression, samples' name should be colnames | |
| # group1, group2 are used to compare two groups of data | |
| # adj.method defines which method used to adjust p values | |
| colnames(data)[1] = "geneSymbol" | |
| # only get samples we wanna to compare, be sure | |
| # all names in group1 and group2 can match colnames of data |
| pltDiff = function(data=NULL, sample=NULL, target=NULL, | |
| group1, group2, group1.name="group1", | |
| group2.name="group2", title="data", x_lab="", y_lab="", | |
| notch=TRUE){ | |
| require(ggpubr, quietly = TRUE) | |
| if(!is.data.frame(data)) stop("Wrong input! Please check your dataset. The input data type must be data.frame.") | |
| a = data.frame(value=data[, target], group=ifelse(!(data[,sample]%in%c(group1,group2)), | |
| NA, ifelse(data[,sample]%in%group1, group1.name, group2.name))) | |
| a = a[a$group%in%c(group1.name, group2.name), ] |
| getID = function(exp_value, method){ | |
| # compute threshold according to method parameter | |
| if(method=="quartile"){ | |
| symbol_stat <- summary(exp_value) | |
| ths1 <- as.numeric(symbol_stat[2]) | |
| ths2 <- as.numeric(symbol_stat[5]) | |
| down_id <- names(exp_value[exp_value<=ths1]) | |
| up_id <- names(exp_value[exp_value>=ths2]) | |
| }else if(method=="mean"){ | |
| ths <- mean(exp_value) |
| #' @function Summary functions for error bar plot. | |
| #' @references http://www.jianshu.com/p/003138ac593b | |
| ## Gives count, mean, standard deviation, standard error of the mean, and confidence interval (default 95%). | |
| ## data: a data frame. | |
| ## 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%) | |
| summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE, |
| "title" "gpl" "bioc_package" "manufacturer" "organism" "data_row_count" | |
| "Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I" "GPL15380" "GGHumanMethCancerPanelv1" "Illumina" "Homo sapiens" 1536 | |
| "Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)" "GPL8490" "IlluminaHumanMethylation27k" "Illumina, Inc." "Homo sapiens" 27578 | |
| "Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)" "GPL13534" "IlluminaHumanMethylation450k" "Illumina, Inc." "Homo sapiens" 485577 | |
| "GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray" "GPL2898" "adme16cod" "GE Healthcare" "Rattus norvegicus" 1280 | |
| "[AG] Affymetrix Arabidopsis Genome Array" "GPL71" "ag" "Affymetrix" "Arabidopsis thaliana" 8297 | |
| "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array" "GPL198" "ath1121501" "Affymetrix" "Arabidopsis thaliana" 22810 | |
| "[Bovine] Affymetrix Bovine Genome Array" "GPL2112" "bovine" "Affymetrix" "Bos taurus" 24128 | |
| "[Canine] Affymetrix Canine Genome 1.0 Array" "GPL39 |
| url | name | user | type | |
|---|---|---|---|---|
| https://bioconductor.org/packages/regioneR | regioneR | NA | Bioconductor | |
| https://bioconductor.org/packages/karyoploteR | karyoploteR | NA | Bioconductor | |
| https://bioconductor.org/packages/metavizr | metavizr | NA | Bioconductor | |
| https://bioconductor.org/packages/IsoformSwitchAnalyzeR | IsoformSwitchAnalyzeR | NA | Bioconductor | |
| https://cran.rstudio.com/packages/UpSetR | UpSetR | NA | CRAN | |
| https://github.com/pachterlab/sleuth | sleuth | pachterlab | github | |
| https://github.com/nekrut/lab_site | lab_site | nekrut | github | |
| https://github.com/bernatgel/karyoploter_tutorial | karyoploter_tutorial | bernatgel | github | |
| https://bitbucket.org/biobakery/metaphlan2 | metaphlan2 | biobakery | github |
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| # --------------------------- | |
| # Accessing the material | |
| # https://tinyurl.com/bioc2017-ELMER | |
| # --------------------------- | |
| library("Bioc2017.TCGAbiolinks.ELMER") | |
| Biobase::openVignette("Bioc2017.TCGAbiolinks.ELMER") | |
| # --------------------------- | |
| # Section 1: | |
| # Aims: |
| # Your init script | |
| # | |
| # Atom will evaluate this file each time a new window is opened. It is run | |
| # after packages are loaded/activated and after the previous editor state | |
| # has been restored. | |
| # | |
| # An example hack to log to the console when each text editor is saved. | |
| # | |
| # atom.workspace.observeTextEditors (editor) -> | |
| # editor.onDidSave -> |