localize

package

v0.0.0-...-40008dc Latest Latest Go to latest Published: Jun 11, 2022 License: MIT Imports: 12 Imported by: 0

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Repository

github.com/knightjdr/cmgo

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README ¶

Module name: `lba-localize`

Localize preys based on enriched terms

parameters	definition	default
enrichment	list of enriched terms for each gene
localization	list of GO IDs that are considered valid localizations
outFilePrimary	output file name for prey localization data	lba-primary.txt

Example file formats

enrichment

symbol	Entrez	Refseq	UniProt	GO ID	GO term	p-value	recall	precision	query size	term size
RBM15	64783	NP_001188474.1	Q96T37	GO:0044428	nuclear part	4.243467e-19	0.01	0.88	50	4521
RBM15	64783	NP_001188474.1	Q96T37	GO:0031981	nuclear lumen	4.508720e-18	0.01	0.84	50	4142
RBM15	64783	NP_001188474.1	Q96T37	GO:0070013	intracellular organelle lumen	6.906764e-14	0.01	0.84	50	5283
RBM15	64783	NP_001188474.1	Q96T37	GO:0043233	organelle lumen	6.906764e-14	0.01	0.84	50	5283
CSNK1G3	1456	NP_001026982.1	Q9Y6M4	GO:0005886	plasma membrane	1.838539e-19	0.01	0.94	50	5539
CSNK1G3	1456	NP_001026982.1	Q9Y6M4	GO:0071944	cell periphery	5.044889e-19	0.01	0.94	50	5662

localization

GO:0005654	nucleoplasm
GO:0005694	chromosome
GO:0005730	nucleolus
GO:0005741	mitochondrial outer membrane
GO:0005743	mitochondrial inner membrane

Output

lba-primary.txt: a file with the GO ID(s) and term name(s) for every prey's assigned localization
lba-profile.txt: matrix showing the precision for each gene across specified localizations. Localizations are in the same order as they are input

Documentation ¶

Overview ¶

Package localize localizes preys using LBA

Index ¶

func Localize(fileOptions map[string]interface{})
type Enrichment

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func Localize ¶

func Localize(fileOptions map[string]interface{})

Localize assigns genes to a compartment and generates a localization profile from enriched terms and a list of valid localizations.

Types ¶

type Enrichment ¶

type Enrichment struct {
	Entrez    string
	ID        string
	Precision float64
	Pvalue    float64
}

Enrichment values relevant to localizing genes.

Source Files ¶

View all Source files

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