转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查

前期的到的基因表达量矩阵,可以得到每个基因的表达量,然而由于我们在做实验过程中的重复(包括技术重复与生物学重复)理论上来讲是可以保持表达量在重复中的一致性。因此我们也可通过这个工作来检查我们是否有正确的重复数据。

Trinity工具包提供了一些可以用于检测重复一致性的脚本。我们今天就通过这些脚本进行检查。

在这个工作之前需要两个数据:

1. 基因表达的counts.matrix 文件
2. 生物学重复的表文件
yeyuntian@yeyuntian-rescuer-r720-15ikbn:~/trinitytest/downstr/RSEMout/RSEMout$ l *counts.matrix
RSEM.gene.counts.matrix  RSEM.isoform.counts.matrix
yeyuntian@yeyuntian-rescuer-r720-15ikbn:~/trinitytest/downstr/RSEMout/RSEMout$ cat samples.txt 
B25 B251
B25 B252
R25 R251
R25 R252
W25 W251
W25 W252
需要注意的是:samples.txt中的名字需要和matrix中的名字一致,否则没办法识别
yeyuntian@yeyuntian-RESCUER-R720-15IKBN:~/Biodata/trinitytest/downstr/RSEMout/RSEMout$ $TRINITY_HOME/Analysis/DifferentialExpression/PtR \ #调用PtR脚本
--matrix RSEM.isoform.counts.matrix \#指定给定的matrix
--samples samples.txt \#样品重复信息
--log2 \#做一个对数处理
--min_rowSums 10 \#过滤数据指标
--compare_replicates #输出的图像参数
为了作为补充,我们获取这个脚本的帮助文件
yeyuntian@yeyuntian-RESCUER-R720-15IKBN:~$ $TRINITY_HOME/Analysis/DifferentialExpression/PtR --help

#################################################################################### 
#
#######################
# Inputs and Outputs: #
#######################
#
#  --matrix         matrix.RAW.normalized.FPKM
#
#  Optional:
#
#  Sample groupings:
#
#  --samples       tab-delimited text file indicating biological replicate relationships.
#                                   ex.
#                                        cond_A    cond_A_rep1
#                                        cond_A    cond_A_rep2
#                                        cond_B    cond_B_rep1
#                                        cond_B    cond_B_rep2
#
#  --gene_factors    tab-delimited file containing gene-to-factor relationships.
#                               ex.
#                                    liver_enriched  gene1
#                                    heart_enriched  gene2
#                                    ...
#                            (use of this data in plotting is noted for corresponding plotting options)
#
#
#  --output         prefix for output file (default: "${matrix_file}.heatmap")
#
#  --save                   save R session (as .RData file)
#  --no_reuse               do not reuse any existing .RData file on initial loading
#
#####################
#  Plotting Actions #
#####################
#
#  --compare_replicates        provide scatter, MA, QQ, and correlation plots to compare replicates.
#
#   
#
#  --barplot_sum_counts        generate a barplot that sums frag counts per replicate across all samples.
#
#  --boxplot_log2_dist         generate a boxplot showing the log2 dist of counts where counts >= min fpkm
#
#  --sample_cor_matrix         generate a sample correlation matrix plot
#    --sample_cor_scale_limits     ex. "-0.2,0.6"
#    --sample_cor_sum_gene_factor_expr     instead of plotting the correlation value, plot the sum of expr according to gene factor
#                                                         requires --gene_factors 
#
#  --sample_cor_subset_matrix   plot the sample correlation matrix, but create a disjoint set for rows,cols.
#                                       The subset of the samples to provide as the columns is provided as parameter.
#
#  --gene_cor_matrix           generate a gene-level correlation matrix plot
#
#  --indiv_gene_cor    generate a correlation matrix and heatmaps for '--top_cor_gene_count' to specified genes (comma-delimited list)
#      --top_cor_gene_count    (requires '--indiv_gene_cor with gene identifier specified')
#      --min_gene_cor_val    (requires '--indiv_gene_cor with gene identifier specified')
#
#  --heatmap                   genes vs. samples heatmap plot
#      --heatmap_scale_limits ""  cap scale intensity to low,high  (ie.  "-5,5")
#      --heatmap_colorscheme   default is 'purple,black,yellow'
#                                      a popular alternative is 'green,black,red'
#                                      Specify a two-color gradient like so: "black,yellow".
#
#     # sample (column) labeling order
#      --lexical_column_ordering        order samples by column name lexical order.
#      --specified_column_ordering   comma-delimited list of column names (must match matrix exactly!)
#      --order_columns_by_samples_file  order the columns in the heatmap according to replicate name ordering in the samples file.
#
#     # gene (row) labeling order
#      --order_by_gene_factor           order the genes by their factor (given --gene_factors)
#
#  --gene_heatmaps     generate heatmaps for just one or more specified genes
#                              Requires a comma-delimited list of gene identifiers.
#                              Plots one heatmap containing all specified genes, then separate heatmaps for each gene.
#                                 if --gene_factors set, will include factor annotations as color panel.
#                                 else if --prin_comp set, will include include principal component color panel.
#
#  --prin_comp            generate principal components, include  top components in heatmap  
#      --add_prin_comp_heatmaps   draw heatmaps for the top  features at each end of the prin. comp. axis.
#                                      (requires '--prin_comp') 
#      --add_top_loadings_pc_heatmap   draw a heatmap containing the  top feature loadings across all PCs.
#      --R_prin_comp_method         options: princomp, prcomp (default: prcomp)
#
#  --mean_vs_sd               expression variability plot. (highlight specific genes by category via --gene_factors )
#
#  --var_vs_count_hist         create histogram of counts of samples having feature expressed within a given expression bin.
#                                              vartype can be any of 'sd|var|cv|fano'
#      --count_hist_num_bins   number of bins to distribute counts in the histogram (default: 10)
#      --count_hist_max_expr   maximum value for the expression histogram (default: max(data))
#      --count_hist_convert_percentages       convert the histogram counts to percentage values.
#
#
#  --per_gene_plots                   plot each gene as a separate expression plot (barplot or lineplot)
#    --per_gene_plot_width      default: 2.5
#    --per_gene_plot_height     default: 2.5
#    --per_gene_plots_per_row    default: 1
#    --per_gene_plots_per_col    default: 2
#    --per_gene_plots_incl_vioplot    include violin plots to show distribution of rep vals
#
########################################################
#  Data Filtering, in order of operation below:  #########################################################
#
#
## Column filters:
#
#  --restrict_samples    comma-delimited list of samples to restrict to (comma-delim list)
#
#  --top_rows          only include the top number of rows in the matrix, as ordered.
#
#  --min_colSums       min number of fragments, default: 0
#
#  --min_expressed_genes            minimum number of genes (rows) for a column (replicate) having at least '--min_gene_expr_val'
#       --min_gene_expr_val    a gene must be at least this value expressed across all samples.  (default: 1)
#
#
## Row Filters:
#
#  --min_rowSums       min number of fragments, default: 0
#
#  --gene_grep      grep on string to restrict to genes
#
#  --min_across_ALL_samples_gene_expr_val    a gene must have this minimum expression value across ALL samples to be retained.
#
#  --min_across_ANY_samples_gene_expr_val    a gene must have at least this expression value across ANY single sample to be retained.
#
#  --min_gene_prevalence    gene must be found expressed in at least this number of columns
#       --min_gene_expr_val    a gene must be at least this value expressed across all samples.  (default: 1)
#
#  --minValAltNA     minimum cell value after above transformations, otherwise convert to NA
#
#  --top_genes         use only the top number of most highly expressed transcripts
#
#  --top_variable_genes       Restrict to the those genes with highest coeff. of variability across samples (use median of replicates)
#
#      --var_gene_method    method for ranking top variable genes ( 'coeffvar|anova', default: 'anova' )
#           --anova_maxFDR     if anova chose, require FDR value <= anova_maxFDR  (default: 0.05)
#            or
#           --anova_maxP     if set, over-rides anova_maxQ  (default, off, uses --anova_maxQ)
#
#  --top_variable_via_stdev_and_mean_expr    perform filtering based on the stdev vs. mean expression plot.
#      Requires both:               (note, if you used --log2 and/or --Zscale, settings below should use those transformed values)
#         --min_stdev_expr        minimum standard deviation in expression
#         --min_mean_expr         minimum mean expression value 
#
######################################
#  Data transformations:             #
######################################
#
#  --CPM                    convert to counts per million (uses sum of totals before filtering)
#  --CPK                    convert to counts per thousand
#
#  --binary                 all values > 0 are set to 1.  All values < 0 are set to zero.
#
#  --log2
#
#  --center_rows            subtract row mean from each data point. (only used under '--heatmap' )
#
#  --Zscale_rows            Z-scale the values across the rows (genes)  
#
#########################
#  Clustering methods:  #
#########################
#
#  --gene_dist         Setting used for --heatmap (samples vs. genes)
#                                  Options: euclidean, gene_cor
#                                           maximum, manhattan, canberra, binary, minkowski
#                                  (default: 'euclidean')  Note: if using 'gene_cor', set method using '--gene_cor' below.
#
#
#  --sample_dist       Setting used for --heatmap (samples vs. genes)
#                                  Options: euclidean, sample_cor
#                                           maximum, manhattan, canberra, binary, minkowski
#                                  (default: 'euclidean')  Note: if using 'sample_cor', set method using '--sample_cor' below.
#
#
#  --gene_clust        ward, single, complete, average, mcquitty, median, centroid, none (default: complete)
#  --sample_clust      ward, single, complete, average, mcquitty, median, centroid, none (default: complete)
#
#  --gene_cor              Options: pearson, spearman  (default: pearson)
#  --sample_cor            Options: pearson, spearman  (default: pearson)
#
####################
#  Image settings: #
####################
#
#
#  --imgfmt            image type (pdf,svg) with default: pdf
#
#  --img_width            image width
#  --img_height           image height
#
################
# Misc. params #
################
#
#  --write_intermediate_data_tables         writes out the data table after each transformation.
#
#  --show_pipeline_flowchart                describe order of events and exit.
#
####################################################################################
但是在这个过程中会报错,原因是本地的R包没有安装好,然后回头去安装R包,有些R包在Bioconductor上有些就在CRAN里面。R脚本如下
source("https://bioconductor.org/biocLite.R")
biocLite("Biobase")
installed.packages()
biocLite("qvalue")
help(package='qvalue')
install.packages('fastcluster')
最后结果就是关于一个处理中生物学重复之间的相关性的几个图,放在一个PDF上的
对于图的讲解有机会再讲。(因为我也不知道有什么意义)我先放出来:
转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第1张图片
image 1 .png

转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第2张图片
image 2 .png

转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第3张图片
image 3 .png

转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第4张图片
image 4 .png
关于这几张图的解释请大家多多指教,另外我后期通过学习也可以晚上对这个图的解读与分析。

=======================

下面进行跨样本间的相关性检测与作图
$TRINITY_HOME/Analysis/DifferentialExpression/PtR \
          --matrix RSEM.isoform.counts.matrix \
          --min_rowSums 10 \
          --samples samples.txt \ #
          --log2 \ #数据转换参数
          --CPM \ #数据转换参数
          --sample_cor_matrix  #输出样品相关性矩阵图
这个代码做出来的结果是不同样本间的数据一致性热图
转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第5张图片
image 5 .png
热图反应处理之间和处理内部的重复之间的一致性

======================

最后一个结果是通过PCA分析对样品重复关系进行检测。
yeyuntian@yeyuntian-RESCUER-R720-15IKBN:~/Biodata/trinitytest/downstr/RSEMout/RSEMout$ $TRINITY_HOME/Analysis/DifferentialExpression/PtR \ 
--matrix RSEM.isoform.counts.matrix \
--samples samples.txt \
--log2 \
--min_rowSums 10 \
--CPM \
--center_rows \
--prin_comp 3
输出结果为PCA分析图(这个图我也看不懂)
转录组分析实战第四节:转录组分析中的技术重复和生物学重复检查_第6张图片
PCA Plot
以后有机会在进行解读吧。

重点是我看不懂这些图,请大家多多指教!

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