README.md

to install

devtools::install_github('hangnoh/flybaseR')

id.converter

Converting or Updating FlyBase IDs or Symbols

Description

The function takes FlyBase IDs (e.g. FBgn0000003) or Gene symbols as an input, and converts it into updated IDs or symbols using the FlyBase ID converter (web). The function accesses FlyBase, so requires internet-connection. FlyBase ID inputs are bundled as 1,000. 100 for symbols. FlyBase IDs for genes that are split into multiple genes will be concatenated with two colons (::). Genes that does not have matching IDs will be shown as "unknown". Certain gene symbols would appear as "unknown" even if the gene exists, and have FlyBase IDs. This is because the ID converter in FlyBase website cannot convert the gene. For example, CG31976 cannot be converted by FlyBase, although you can find the gene from the gene report. Setting diehard.symbols = T will look for gene report pages of such unconvertible genes one by one. The process is essentially slow because it accesses FlyBase for each gene.

Usage

id.converter(x, symbols = F, bundle.size = 1000, DmelOnly = T, polite.access = 0, diehard.symbols = F, convert.into)

Arguments

Examples

id.converter(x, symbols = T)
id.converter(x, bundle.size = 50, polite.access = 10, convert.into = "transcripts")
id.converter(x, symbols = T, bundle.size = 50, diehard.symbols = T)

id.converter2

Updating FlyBase IDs to a certain version.

Description

The function takes FlyBase IDs (e.g. FBgn0000003) as an input, and converts it into certain versions of IDs. This function is not able to handle gene symbols. The function accesses the FlyBase FTP site, so requires internet-connection. FlyBase IDs for genes that are split into multiple genes will be concatenated with two colons (::). Genes that does not have matching IDs will be shown as "unknown".

Usage

id.converter2(x, version, thread = 1)

Arguments

Examples

id.converter2(x, version=6.12)
id.converter2(x, version="FB2016_04", thread=4)

j2g

Open FlyBase gene reports using a web browser

Description

The function takes FlyBase IDs (e.g. FBgn0000003) or Gene symbols as an input, and opens FlyBase gene report from the default web browser (e.g. Jump2Gene).

Usage

j2g(x, n = 10)

Arguments

Examples

j2g("e2f")
j2g(c("ovo", "otu"))
j2g("FBgn0000504")
j2g(c("FBgn0000504", "tra"))


hangnoh/flybaseR documentation built on Jan. 7, 2020, 4:20 a.m.