Gather Expressions for TCGA Datasets

Function gathers expressions over multiple TCGA datasets and extracts expressions for desired genes. See rnaseq, mRNA, RPPA, miRNASeq, methylation.

expressionsTCGA(..., extract.cols = NULL, extract.names = TRUE)

Arguments

...

A data.frame or data.frames from TCGA study containing expressions informations.

extract.cols

A character specifing the names of columns to be extracted with bcr_patient_barcode. If NULL (by default) all columns are returned.

extract.names

Logical, whether to extract names of passed data.frames in ....

Note

Input data.frames should contain column bcr_patient_barcode if extract.cols is specified.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

See also

RTCGA website http://rtcga.github.io/RTCGA/articles/Visualizations.html.

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, createTCGA, datasetsTCGA, downloadTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, mutationsTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA

Examples

## for all examples
library(dplyr)
library(tidyr)
library(ggplot2)

## RNASeq expressions
library(RTCGA.rnaseq)
expressionsTCGA(BRCA.rnaseq, OV.rnaseq, HNSC.rnaseq,
               extract.cols = "VENTX|27287") %>%
  rename(cohort = dataset,
         VENTX = `VENTX|27287`) %>%
 filter(substr(bcr_patient_barcode, 14, 15) == "01") %>% #cancer samples
  ggplot(aes(y = log1p(VENTX),
             x = reorder(cohort, log1p(VENTX), median),
             fill = cohort)) +
  geom_boxplot() +
  theme_RTCGA() +
  scale_fill_brewer(palette = "Dark2")
#> Scale for 'fill' is already present. Adding another scale for 'fill', which
#> will replace the existing scale.

## mRNA expressions  
library(tidyr)
library(RTCGA.mRNA)
expressionsTCGA(BRCA.mRNA, COAD.mRNA, LUSC.mRNA, UCEC.mRNA,
               extract.cols = c("ARHGAP24", "TRAV20")) %>%
  rename(cohort = dataset) %>%
  select(-bcr_patient_barcode) %>%
  gather(key = "mRNA", value = "value", -cohort)  %>%
  ggplot(aes(y = value,
             x = reorder(cohort, value, mean),
             fill = cohort)) +
  geom_boxplot() +
  theme_RTCGA() +
  scale_fill_brewer(palette = "Set3") +
  facet_grid(mRNA~.) +
  theme(legend.position = "top")
#> Scale for 'fill' is already present. Adding another scale for 'fill', which
#> will replace the existing scale.
#> Warning: Removed 2 rows containing non-finite values (stat_boxplot).


## RPPA expressions
library(RTCGA.RPPA)
expressionsTCGA(ACC.RPPA, BLCA.RPPA, BRCA.RPPA,
    extract.cols = c("4E-BP1_pS65", "4E-BP1")) %>%
  rename(cohort = dataset) %>%
  select(-bcr_patient_barcode) %>%
  gather(key = "RPPA", value = "value", -cohort)  %>%
  ggplot(aes(fill = cohort,
             y = value,
             x = RPPA)) +
  geom_boxplot() +
  theme_dark(base_size = 15) +
  scale_fill_manual(values = c("#eb6420", "#207de5", "#fbca04")) +
  coord_flip() +
  theme(legend.position = "top") +
  geom_jitter(alpha = 0.5, col = "white", size = 0.6, width = 0.7)



## miRNASeq expressions 
library(RTCGA.miRNASeq)
# miRNASeq has bcr_patienct_barcode in rownames...
mutate(ACC.miRNASeq,
   bcr_patient_barcode = substr(rownames(ACC.miRNASeq), 1, 25)) -> ACC.miRNASeq.bcr
mutate(CESC.miRNASeq,
   bcr_patient_barcode = substr(rownames(CESC.miRNASeq), 1, 25)) -> CESC.miRNASeq.bcr
mutate(CHOL.miRNASeq,
   bcr_patient_barcode = substr(rownames(CHOL.miRNASeq), 1, 25)) -> CHOL.miRNASeq.bcr
mutate(LAML.miRNASeq,
   bcr_patient_barcode = substr(rownames(LAML.miRNASeq), 1, 25)) -> LAML.miRNASeq.bcr
mutate(PAAD.miRNASeq,
   bcr_patient_barcode = substr(rownames(PAAD.miRNASeq), 1, 25)) -> PAAD.miRNASeq.bcr
mutate(THYM.miRNASeq,
   bcr_patient_barcode = substr(rownames(THYM.miRNASeq), 1, 25)) -> THYM.miRNASeq.bcr
mutate(LGG.miRNASeq,
   bcr_patient_barcode = substr(rownames(LGG.miRNASeq), 1, 25)) -> LGG.miRNASeq.bcr
mutate(STAD.miRNASeq,
   bcr_patient_barcode = substr(rownames(STAD.miRNASeq), 1, 25)) -> STAD.miRNASeq.bcr


expressionsTCGA(ACC.miRNASeq.bcr, CESC.miRNASeq.bcr, CHOL.miRNASeq.bcr,
             LAML.miRNASeq.bcr, PAAD.miRNASeq.bcr, THYM.miRNASeq.bcr,
             LGG.miRNASeq.bcr, STAD.miRNASeq.bcr,
  extract.cols = c("machine", "hsa-mir-101-1", "miRNA_ID")) %>%
                rename(cohort = dataset) %>%
   filter(miRNA_ID == "read_count") %>%
   select(-bcr_patient_barcode, -miRNA_ID) %>%
   gather(key = "key", value = "value", -cohort, -machine) %>%
   mutate(value = as.numeric(value)) %>%
   ggplot(aes(x = cohort,
              y = log1p(value),
              fill = as.factor(machine)) )+
   geom_boxplot() +
   theme_RTCGA(base_size = 13) +
   coord_flip() +
   theme(legend.position = "top") +
   scale_fill_brewer(palette = "Paired") +
   ggtitle("hsa-mir-101-1")
#> Scale for 'fill' is already present. Adding another scale for 'fill', which
#> will replace the existing scale.