Enrichment-test
Enrichment test based on PCA loadings
Required packages:
allez; in bash run R CMD INSTALL allez.tar.gz
.db pkgs; in R run
source("http://bioconductor.org/biocLite.R")
biocLite("org.Hs.eg.db”)
biocLite("org.Mm.eg.db”)
biocLite("GO.db")
Example commands to run the script:
- Rscript Enrich.R ExampleLoading.csv MarkerLists.csv
- Rscript Enrich.R ExampleLoading.txt MarkerLists.txt
- Rscript Enrich.R ExampleLoading.csv
- Rscript Enrich.R ExampleLoading.txt MarkerLists.txt 20
- Rscript Enrich.R ExampleLoading.txt MarkerLists.txt 20 500
- Rscript Enrich.R ExampleLoading.txt MarkerLists.txt 20 500 mouse T
The 3rd term indicates the name of the loadings (or other scores). The file should contain only one column. Row names should be gene names. Each entry represents loading (or score) of that particular gene. Currently the program takes csv files or tab delimited file. The input file will be treated as a tab delimited file if the suffix is not '.csv'.
The 4th term defines the marker lists of interest. It could be csv or tab delimited file. Each row represents a marker list. Row names are the list names. The number of columns should be N, in which N is the number of genes in the longest list. For lists with length M - N, the M+1, ..., N's column in that row should be filled with "" or " ". If the 4th term is not specified, only GO terms will be considered.
The 5th (6th) term defines the threshold to filter out small(large) sets. Default is 10 (800). Sets that are smaller (larger) than the threshold are not considered.
The 7th term defines what annotation package to use. It could be either 'human' or 'mouse'
The 8th term defines whether one-tailed p value should be calculated. If the input values are absolute values, then it should be specified as "T". Otherwise it should be specified as "F", in which case two-tailed p values will be calculated. This option is only valid in the allez implementation (not in EACI or EASE).
Outputs:
XX_allsets.txt: enrichment results of all gene sets (GO sets + local sets).
XX_localsets.txt: enrichment results of only local sets. The summary statistics of these sets are the same as those in the XX_allsets.txt
The output files contain GO term (NA for local sets), set p value, adjusted p value, z score, set size, set mean and set sd. Sets are sorted by p value. Sets with large absoloute z scores are expected to have small p values.
EACI test
Install EACI package:
in bash
run R CMD INSTALL EACI_0.0.1.tar.gz
Example commands to run the script:
- Rscript Enrich_eaci.R ExampleLoading.csv MarkerLists.csv
- Rscript Enrich_eaci.R ExampleLoading.txt MarkerLists.txt
- Rscript Enrich_eaci.R ExampleLoading.csv
- Rscript Enrich_eaci.R ExampleLoading.csv MarkerLists.csv 20
- Rscript Enrich_eaci.R ExampleLoading.csv MarkerLists.csv 20 500
- Rscript Enrich_eaci.R ExampleLoading.csv MarkerLists.csv 20 500 mouse
Outputs
XX_EACIenrichment_allsets.txt
XX_EACIenrichment_localsets.txt
David EASE score
Calculate David EASE score for enrichment analysis
Th EASE scores implementation is available in EACI_0.0.1.tar.gz as well.
Example commands to run the script:
- Rscript Enrich_eaci.R ExampleLoading_binary.csv MarkerLists.csv
- Rscript Enrich_eaci.R ExampleLoading_binary.csv
- Rscript Enrich_eaci.R ExampleLoading_binary.csv MarkerLists.csv 20
- Rscript Enrich_eaci.R ExampleLoading_binary.csv MarkerLists.csv 20 500
- Rscript Enrich_eaci.R ExampleLoading_binary.csv NULL 20 500
- Rscript Enrich_eaci.R ExampleLoading_binary.csv NULL 20 500 mouse
Note the input file for EASE score calculation should contains binary scores. 1 for Significant and 0 for non-significant
Outputs
XX_DavidEASEenrichment_localsets.txt
XX_DavidEASEenrichment_allsets.txt