crapome

package
v0.0.0-...-40008dc Latest Latest
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 Go to latest Published: Jun 11, 2022 License: MIT Imports: 14 Imported by: 0

README

Module name: summary-crapome

Generates a CRAPome matrix from SAINT input files

parameters definition default
baitFiles bait.dat: files with bait sample IDs, bait name and control status (C: control, T: non-control)
crapomeID text file with two columns containing sample name with ID as ID_name and CRAPome CC number
interactionFiles inter.dat: files with bait ID and name, prey accession and spectral count
outFile output matrix crapome-matrix.txt
preyFiles prey.dat: files with prey accession, sequence length and gene name

Multiple SAINT tasks can be merged by listing multiple bait.dat, inter.dat and prey.dat files separated by a semicolon. Each of these should be listed in a consistent order:

-baitFiles="bait-task1.dat;bait-task2.dat" -interactionFiles="inter-task1.dat;inter-task2.dat" -preyFiles="prey-task1.dat;prey-task2.dat"

Example file formats

baitFile (bait.dat)

header: projectID_sampleID | bait name | control status

128_468	ACTB	T
128_492	ACTB	T
128_590	ATP2A1	T
128_546	ATP2A1	T
128_737	737_BirAFLAG	C
128_825	825_BirAFLAG	C
crapomeID
filename	cc
9522_BirAFLAG_April2017_Go_RIPA_07012018.raw	CC1100
9221_BirAFLAG_HighDen_Go_KA_RIPA_10112017_BR1.raw	CC1101
7909_BirAFLAG_April2017_Go_RIPA_06042017_TR1.raw	CC1102
7024_BirAFLAG_May2016_test_Go_RIPA_31102016_TR1	CC1103
7015_BirAFLAG_May2016_Go_RIPA_31102016_TR1.raw	CC1104
interactionFile (inter.dat)

header: projectID_sampleID | bait name | prey accession | spectral count | unique peptides |

128_468	ACTB	BirA_R118G_H0QFJ5	1410	23
128_468	ACTB	NP_000029.2	4	3
128_468	ACTB	NP_000108.1	2	2
128_468	ACTB	NP_000280.1	3	2
128_468	ACTB	NP_000402.3	11	10
128_468	ACTB	NP_000652.2	7	5
preyFile (prey.dat)

header: accession | prey sequence length | prey name |

BirA_R118G_H0QFJ5	321	BirA_R118G_H0QFJ5
NP_000029.2	2843	APC
NP_000108.1	254	EMD
NP_000280.1	780	PFKM
NP_000402.3	726	HLCS
NP_000652.2	192	RPL9
NP_000911.2	1178	PC
Output
  • txt matrix file formatted for CRAPome with prey summaries across control samples

Documentation

Overview

Package crapome generates a CRAPome matrix from SAINT input files.

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Matrix 

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

Matrix reads SAINT input files and generates a CRAPome matrix.

Types

This section is empty.

Source Files

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