Package 'AnnoProbe'

Annotate gene IDs according to GTF files in gencode

Description

annoGene will return a data.frame of gene information or write them to a file (csv or html format). The user should set a list of genes to be annotated, with "ENSEMBL" or "SYMBOL" style.

Usage

annoGene(IDs, ID_type, species = "human", out_file)

Arguments

IDs	a list of genes
ID_type	the type of input IDs, should be "ENSEMBL" or "SYMBOL"
species	choose human or mouse, or rat, default: human
out_file	the filename, should be ".csv" or ".html".

Value

a dataframe which columns contain genesymbol, biotypes, ensembl ids and the positions of genes

Examples

IDs <- c("DDX11L1", "MIR6859-1", "OR4G4P", "OR4F5")
ID_type = "SYMBOL"
annoGene(IDs, ID_type)
annoGene(IDs, ID_type,out_file ='tmp.html')
annoGene(IDs, ID_type,out_file ='tmp.csv')

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Check a list of genes how they show difference.

Description

How does a gene or a list of genes show difference between two group. The boxplot or heatmap will be drawed. just a wrap function of ggpubr and pheatmap.

Usage

check_diff_genes(gene, genes_expr, group_list)

Arguments

gene	A vector contains all gene ids of interest. Gene ids should be gene symbol.
genes_expr	An expression matrix, the rownames should be gene symbol.
group_list	A vector contains the group information of each samples in expression matrix

Value

A figure : boxplot or heatmap

Examples

attach(GSE95166)
check_diff_genes('NKILA',genes_expr,group_list )
x=DEG$logFC
names(x)=rownames(DEG)
cg=c(names(head(sort(x),100)),  names(tail(sort(x),100)))
check_diff_genes(cg,genes_expr,group_list )

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Check whether the input gpl in our platform list or not

Description

Check whether the input gpl in our platform list or not

Usage

checkGPL(GPL = NULL)

Arguments

GPL	GPL(GEO platform) number, eg: GPL570

Value

returns a boolean value

Examples

checkGPL('GPL570')
checkGPL('GPL15314')
checkGPL('GPL10558')

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draw a heatmap for DEG result

Description

deg_heatmap will draw a heatmap for you.

Usage

deg_heatmap(deg, genes_expr, group_list, topn = 20)

Arguments

deg	the result from limma.
genes_expr	the expression matrix
group_list	a vector
topn	the number of genes in heatmap, default:20

Value

a ggplot2 style figure.

Examples

attach(GSE27533)
deg_heatmap(DEG,genes_expr)

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draw a volcano for DEG result

Description

deg_volcano will draw a volcano for you.

Usage

deg_volcano(need_deg, style = 1, p_thred = 0.05, logFC_thred = 1)

Arguments

need_deg	should be 3 columns : gene, logFC, p.value(or p.adjust
style	you can try 1 or 2, default: 1
p_thred	default:0.05
logFC_thred	default:1

Value

a ggplot2 style figure.

Examples

deg=GSE27533$DEG
need_deg=data.frame(symbols=rownames(deg), logFC=deg$logFC, p=deg$P.Value)
deg_volcano(need_deg,1)
deg_volcano(need_deg,2)

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Filter expression matrix based on annotation

Description

filterEM will annotate the probes in expression matrix and remove the duplicated gene symbols. because there will be many probes mapped to same genes, we will only keep the max value one.

Usage

filterEM(probes_expr, probe2gene)

Arguments

probes_expr	is an expression matrix which rownames are probes of probe2gene and each column is a sample
probe2gene	the first column is probes and the second column is corresponding gene symbols

Value

a expression matrix which has been filtered duplicated gene symbols

Examples

attach(GSE95166)
head(probes_expr)
head(probe2gene)
genes_expr <- filterEM(probes_expr,probe2gene)
head(genes_expr)

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Download expression dataset by GSE id

Description

geoChina will download the expression matrix and phenotype data as ExpressionSet format from cloud in mainland China, it's a alternative method for getGEO function from GEOquery package. geoChina('gse1009') is the same as eSet=getGEO('gse1009', getGPL = F)

Usage

geoChina(gse = "GSE2546", mirror = "tercent")

Arguments

gse	input GSE id, such as GSE1009, GSE2546, default:GSE2546

Value

a list of ExpressionSet, which contains the expression matrix and phenotype data

Examples

geoChina()
geoChina('gse1009')
geoChina('GSE1009')

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Get all GPL list in our package getGPLList returns all the GPL number checklist stored in package

Description

Get all GPL list in our package getGPLList returns all the GPL number checklist stored in package

Usage

getGPLList()

Value

a data.frame which contains the gpl and name of array.

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Get Probe Annotation

Description

getGPLAnno returns probe annotations for input gpl

Usage

idmap(gpl = "GPL570", type = "bioc", mirror = "tercent")

Arguments

GPL	GPL(GEO platform) number, eg: GPL570
source	source of probe anntation stored, one of "pipe", "bioc", "soft", default:"pipe"

Value

probe annotaions

Examples

ids=idmap('GPL570')
ids=idmap('GPL570',type='soft')
ids=idmap('GPL18084',type='pipe')

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Print GPL information

Description

Print GPL information

Usage

printGPLInfo(GPL = NULL)

Arguments

GPL	GPL(GEO platform) number, eg: GPL570

Value

print detail information of the input GEO platform

Examples

printGPLInfo('GPL93')

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