genedist: Chromosomal distribution of the genes in the selected geneset

In GSAQ: Gene Set Analysis with QTL

Description

The function computes the chromosome wise distribution of the genes in the selected geneset and also plots the chromosomal distribution.

Usage

genedist(geneset, genelist, plot)

Arguments

geneset	geneset is a vector of characters representing the names of genes/ gene ids selected from the whole gene list by using a gene selection method.
genelist	genelist is a N by 3 dataframe/ matrix (genes/gene ids as row names); where, N represents the number of genes in the whole gene space: first coloumn represnting the chromosomal location of genes: second coloumn representing the start position of genes in terms of basepairs: third coloumn representing the end position of genes in terms of basepairs in their respective chromosomes.
plot	plot is a character string indicating whether the chromosomal distribution of the genes in the selected geneset will be plotted or not. It can be either TRUE/FALSE.

Value

The function returns the chromosomal distribution of the genes in the selected geneset.

Author(s)

Samarendra Das

Examples

data(rice_salt)
data(genelist)
x=as.data.frame(rice_salt[-1,])
y=as.numeric(rice_salt[1,])
geneset= GeneSelect(x, y, s=50, method="t-score")$selectgenes
genelist=as.data.frame(genelist)
genedist(geneset, genelist, plot=TRUE)

Example output

                  Gene ID Chr. No. Start Position (bp) End Position (bp)
1    OsAffx.18823.1.S1_at       11             7244090           7244585
2        Os.52357.1.S1_at       10              790405            791375
3      Os.57545.1.S1_x_at        2            30382128          30383271
4      Os.27237.1.A1_a_at       10            22529878          22533205
5        Os.15665.1.S1_at        7            28832613          28834725
6        Os.11919.1.S1_at        1            40973409          40974780
7   OsAffx.5266.1.S1_x_at        7             5120621           5121029
8    OsAffx.28630.1.S1_at        7            16192183          16193513
9        Os.26728.3.S1_at       10            19556177          19558472
10   OsAffx.14372.2.S1_at        4            30910574          30913653
11       Os.57517.1.S1_at        9            20395980          20396173
12  OsAffx.6163.1.S1_x_at        9             1890089           1890491
13       Os.19822.1.S1_at        3             4987876           4992411
14    OsAffx.9461.1.S1_at        1            34571693          34574407
15   OsAffx.31668.1.S1_at       12             5184492           5185959
16   OsAffx.24056.2.S1_at        1            37281170          37285279
17       Os.24287.1.A1_at        4            31895292          31900168
18        Os.8957.1.S1_at        1            36540163          36545196
19       Os.50892.1.S1_at        9            15212405          15215467
20  OsAffx.3973.1.S1_x_at        4            19280318          19281434
21      Os.6141.1.S1_s_at        7             3847011           3850322
22    OsAffx.5284.1.S1_at        7             5744864           5749784
23    OsAffx.7406.1.S1_at       11            26774245          26775075
24       Os.49199.1.S1_at        2             6559487           6562188
25      Os.7388.2.S1_x_at        7             3465606           3469077
26       Os.17465.1.S1_at        7             5877158           5877858
27   OsAffx.15802.1.S1_at        6            22292245          22301030
28       Os.14770.1.S1_at        3             9878093           9880793
29       Os.53064.1.S1_at        6             4424637           4425671
30   OsAffx.25841.1.S1_at        4              967142            967556
31   OsAffx.17895.1.S1_at        9            15430675          15431149
32   OsAffx.30771.1.S1_at       12              483986            487778
33       Os.27839.1.S1_at        5            22770096          22774082
34       Os.23660.1.S2_at        7              535601            537773
35 OsAffx.21997.3.S1_x_at        8            25610345          25616012
36        Os.8545.1.S1_at        1            11316608          11320062
37       Os.52757.1.S2_at        4            14821362          14826775
38       Os.52011.1.S1_at        4            23083334          23085438
39       Os.49488.1.S1_at        7             3111649           3113960
40 OsAffx.12573.1.S1_s_at        2            30650261          30651129
41       Os.11237.1.S1_at        3            10391656          10392766
42       Os.13516.1.S1_at       12             2535926           2538878
43  OsAffx.8465.1.S1_x_at       10             4492104           4492797
44       Os.24329.1.A1_at        4             9995573           9996239
45 OsAffx.28033.1.S1_x_at        6            24502481          24507315
46   OsAffx.22281.1.S1_at        3             6566148           6570203
47      Os.9515.3.S1_x_at        7             4499106           4501911
48    OsAffx.5106.1.S1_at        6            26960703          26961368
49       Os.53924.1.S1_at        7            22648365          22654350
50   OsAffx.18359.1.S1_at       10            12119637          12120071

GSAQ documentation built on May 2, 2019, 9:34 a.m.