Package 'easyDifferentialGeneCoexpression'

Function that computes the differential coexpression of a list of probesets in a specific dataset and returns the most significant pairs

Description

Function that computes the differential coexpression of a list of probesets in a specific dataset and returns the most significant pairs

Usage

easyDifferentialGeneCoexpression(
  list_of_probesets_to_select,
  GSE_code,
  featureNameToDiscriminateConditions,
  firstConditionName,
  secondConditionName,
  batchCorrection = TRUE,
  verbose = FALSE
)

Arguments

list_of_probesets_to_select	list of probesets for which the differential coexpression should be computed
GSE_code	GEO accession code of the dataset to analyze
featureNameToDiscriminateConditions	name of the feature of the dataset that contains the two conditions to investigate
firstConditionName	name of the first condition in the feature to discriminate (for example, "healthy")
secondConditionName	name of the second condition in the feature to discriminate (for example, "cancer")
batchCorrection	says if the script should perform the batch correction with limma::removeBatchEffect() or not
verbose	prints all the intermediate message to standard output or not

Value

a dataframe containing the significantly differentially co-expressed pairs of genes

Examples

probesetList <- c("200738_s_at", "217356_s_at", "206686_at")
verboseFlag <- "TRUE"
batchCorrection <- "TRUE"
signDiffCoexpressGenePairs <- easyDifferentialGeneCoexpression(probesetList, 
"GSE3268", "description", "Normal", "Tumor", verboseFlag)

---

Function that associates a gene symbol to a probeset for some Affymetrix platforms

Description

Function that associates a gene symbol to a probeset for some Affymetrix platforms

Usage

fromProbesetToGeneSymbol(
  thisProbeset,
  thisPlatform,
  this_platform_ann_df,
  verbose = FALSE
)

Arguments

thisProbeset	probeset in input
thisPlatform	GEO platform accession code
this_platform_ann_df	annotation dataframe of the platform
verbose	prints all the intermediate message to standard output or not

Value

a gene symbol as string

---

Function that downloads gene expression data from GEO, after checking the connection

Description

Function that downloads gene expression data from GEO, after checking the connection

Usage

geoDataDownload(GSE_code, verbose = FALSE)

Arguments

GSE_code	GEO code dataset
verbose	prints all the intermediate message to standard output or not

Value

a gene set gene expression AnnotationDataFrame

---

Function that downloads the annotations of a GEO platform

Description

Function that downloads the annotations of a GEO platform

Usage

geoPlatformAnnotationsDownload(platformID, verbose = FALSE)

Arguments

platformID	GEO platform ID
verbose	prints all the intermediate message to standard output or not

Value

a dataframe containing the annotations of the GEO platform

---

Function that reads a CSV file of probesets or gene symbols and, in the latter case, it retrieves the original probesets

Description

Function that reads a CSV file of probesets or gene symbols and, in the latter case, it retrieves the original probesets

Usage

probesetRetrieval(
  probesets_or_gene_symbols,
  csv_file_name,
  platformCode,
  verbose = FALSE
)

Arguments

probesets_or_gene_symbols	flag saying if we're reading probesets or gene symbols
csv_file_name	complete name of CSV file containing the probesets or the gene symbols
platformCode	code of the microarray platform for which the probeset-gene symbol mapping should be done
verbose	prints all the intermediate message to standard output or not

Value

a vector of probesets

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